Unofficial Nielsen Lab Manual - The University of Texas at Dallas
Contents
1. Transfer 4 s Growing 0 10 E 3 3 L E 20 30 t 0 10 20 30 40 50 60 Transfer 29 7155 R Angstroms Growing 33 4609 Figure 6 Plot of nanoparticle solvation free energies generated using Xmgrace Xmgrace or just Grace is a GUI Graphical User Interface plotting program for generating 2 D plots Xmgrace has many other features besides just plotting e g data integration histogram curve fitting etc Xmgrace is the lab choice for generating publication quality 2 D plots Xmgrace can be started from the terminal using the xmgrace command To learn more and find links to downloads and useful information visit the Grace website at http plasma gate weizmann ac il Grace 6 Other Useful Programs Applications and Tools In addition to simulation modeling and plotting software there are many other programs applications and tools that are available and are can be used in the lab Some of these are discussed below 20 6 1 pdflatex pdflatex is a program that allows you to compile LaTeX code see Section 7 6 into PDF Portable Document Format files pdflatex can be executed from the terminal using pdflatex filename tex and will generate a file named filename pdf To learn more visit http www math rug nl 1simftrentelman jacob pdflatex pdi 6 2 POV Ray flatex html Figure 7 Image of a simulation system generated using POV Ray POV Ray or the Persistence of Vision Raytracer2. will copy a sub directory under my current work ing directory to my home directory mv lt source gt lt destination gt Move or rename files The same command is used for moving and renaming files and directories Continued on next page Table 3 continued from previous page rm lt files gt Remove delete files You must own the file in order to be able to remove it On many systems you will be asked for confir mation of deletion if you don t want this use the f force option e g rm f will remove all files in my current working directory no questions asked mkdir lt directory gt Make a new directory rmdir lt directory gt Remove an empty directory rm r files recursive remove Remove files directories and their sub directories Careful with this command as root you can easily remove all files on the system with such a command executed on the top of your directory tree and there is no undelete in Linux yet But if you really wanted to do it reconsider here is how as root rm rf cat filename more View the content of a text file called filename one page a time The is the pipe symbol on many American keyboards it shares the key with The pipe makes the output stop after each screenful For long files it is sometimes convenient to use the commands head and tail that display
3. It is often a good choice for scripting latex writing etc With the use of plug ins gedit can be extended into 10 a more powerful editor gedit is launched by either the menu or through the terminal by entering gedit To read more about gedit visit the gedit website https projects gnome org gedit Emacs is a platform independent program which has a huge following Another program which is omnipotent and can be used to do all of the things that gedit can do and a lot more including compiling and link ing programs etc Emacs is also launched by either the menu Application Acessories Emacs Text Editor or through the terminal with the emacs command To learn more about Emacs visit the Emacs website http www gnu org software emacs The use of Emacs and gedit are much more intuitive but the use of vi is not so a separate section is dedicated to its use 2 4 1 VI Usage To edit a text file in VI launch VI passing the text file as an argument e g to edit a file myfile txt use jbs072000 animal vi myfile txt This should take you into a blank screen which is actually in the VI program VI has a few modes it loads into Command Mode which is progressively more useful the more VI commands you use To use VI like a conventional text editor press the Insert key once and the status line at the bottom of the screen should turn into IN SERT which lets you know that you are in Insert Mode w
4. jbs072000 animal ssh X Y jbs072000 bigbird utdallas edu Which should give the follwing output University of Texas at Dallas Natural Sciences and Mathematics Pursuant to Texas Administrative Code 202 Unauthorized use is prohibited Usage may be subject to security testing and monitoring Misuse is subject to criminal prosecution and No expectation of privacy except as otherwise provided by applicable privacy laws jos072000 bigbird utdallas edu s password At which point enter your password and the login will be complete The terminal can also be used to log onto other machines in the lab which is useful if you need to run a job or program on a computer that is not being used The same process used to log onto bigbird can be used to log onto the computers in the lab e g jbs072000 animal ssh X Y jbs072000 lt computername gt will log you into any computer in the lab There is also a shortcut version of the command that can be used for the in lab computers which is Jbs072000O animal ssh lt computername gt The system can also be remotely accessed outside of the campus You will need a computer with a terminal from which you can log in To log onto bigbird requires the same command as in the earlier bigbird example However the NSM system is accessed by using john home ssh X Y jbs072000 apache utdallas edu Once you are logged onto apache you can then remotely log into any of the other in lab
5. t hesitate to add to or change it 2 Computational Resources 2 1 In Lab There are currently 5 machines in the lab They are listed below Name Processor Number of CPUs Architecture bert Xeon 16 64 bit cvc Xeon 24 64 bit animal core 2 2 64 bit piggy quadcore 4 64 bit grover pentium D 2 64 bit Table 1 List of machines available in the lab 2 2 Out of Lab The lab also has access to a CPU cluster for more computationally intensive simulations programs However the cluster is not physically located in the lab and must be accessed through remote logging The master node of this cluster is named bigbird and is a 64 bit machine bigbird has 24 on board CPUs along with a Tesla scientific grade GPU Graphics Processing Unit The additional CPUs in the cluster are partitioned into 4 nodes b1 b2 b2 and b4 each with 32 cpus Each node can be logged into directly and have programs jobs run or can have jobs partitioned to them from bigbird using the job queue system 2 3 Environment All the machines use Linux The Linux implementation depends on the machine but the computer network has been setup so you can log into any machine in the Nielsen lab and still have your files preserved In this sense it does not matter which machine you use You can also remotely log in to and use any other lab machine from whichever machine you are at All the machines currently available are 64 bit
6. GIMP visit the website http www gimp org 22 6 4 tmux RNAME PRI NIC G_EXITING NULL G NULL 8 F1 tmux imsg 12diff diff 7 134 0 Hg Diff Figure 9 Screenshot of tmux setup tmux is a free open source terminal multiplexer which allows the user to split terminal window and run multiple programs or tools at the same time It allows for easy switching between the windowpanes and reduces the need for multiple tabs and or separate instances of the terminal to multi task tmux can be very useful However it does require the use of keyboard commands bindings to navigate and perform tmux functions Thus it takes a little time to get used to working in For more information links to the manual source code and more visit the Source Forge page for tmux at http tmux sourceforge net Note An alternative to tumux is GNU screen which has many features similar to tmux To learn more about GNU screen visit http www gnu org software screen 23 6 5 Mathematica ParametricPlot3D uCos u 4 Cos vYy u uSin u 4 Cos y u uSin y u fu O 4Pi Y O 2Pi PlotPoints gt 60 12 Graphics3D Figure 10 3 D plot generated using Mathematica Mathematica is very powerful computational program developed by Wolfram It has many abilities from taking derivatives and doing integration to 2 D and 3 D plotting and much more Mathematica is a com mercial software and is not free However UT
7. containing extensions to in many cases to perform structure refine ment simple simulations and many other things The visualization program that is most often used in the lab 17 is called VMD Another popular molecular modeling software is called Maestro Maestro is developed and distributed by the company Shr dinger like the equation and can be downloaded for free under an academic liscence The associated webpage is http www schrodinger comproductpage 14 12 4 1 VMD Figure 4 Image of surfactant peptides interaction with a carbon nanotube in water generated by VMD VMD or Visual Molecular Dynamics is a powerful molecular modeling program primarily for displaying animating and analyzing molecular systems VMD is the choice modeling program of the lab It is devel oped and distributed by the TCB Theoretical and Computational Biophysics Group at the University of Illinois Urbana Champaign It is a companion program to NAMD but does not require NAMD except to do real time interactive NAMD simulations and can be used to visualize many different coordinate trajectory file types from different simulation codes VMD uses 3 D graphics and offers many extensions and func tions The code is free to download and is open source VMD supports a scripting interface in both TcL Tool Comand Language and Python languages VMD has a large library of scripting functions built in 18 which can be used in conjunction with the normal T
8. discrete time step It is assumed that the forces acting on the atoms do not change during this time step and hence the time step is necessarily small in the femto second range 10715 s The computer does this loop continuously updating the force and velocity of each atom then updating their positions to obtain a trajectory of the system The information contained in the trajectory allows the calculation of thermodynamic quantities such as free energies partition co efficients diffusion constants etc Apart from measuring quantities molecular dynamics allows us to have a microscope of infinite resolution because Heisenberg has no say here and see physical processes occurring at the molecular scale The main limitation on molecular dynamics is that electronic structure of atoms is treated explicitly hence it is not a good method to study systems where there is rearrangement of electrons such as chemical reactions where covalent bonds are formed redox reaction etc Although newer molecular dynamics have been developed to allow simulation of systems with explicit electron rearrangement the majority of simu lation studies are carried out on physical phenomena A concept central to the ability to calculate the forces acting on atoms through a classical mechanics frame work is that of a force field The force field decomposes the structure energy relationship of molecules and atoms into several components both bonded and non bonded In
9. essence the force field gives us a way 29 to calculate the energy of the system as a function of the spatial coordinates positions of the atoms usually through simple mathematical forms In general since the force acting on any particle in a given system depends on all atoms in the system the number of calculations needed for one time step increases with N where N is the number of atoms in the system Therefore there is a practical limit to the size of the systems we can look at for how many time steps we can run the trajectory for This fact also manifest in a compromise in the details we include in the atomic description of the molecules in the system and the time it takes to simulate With conventional computational systems in 2011 researchers in the molecular dynamics field often study systems in the scale of hundreds of nanometers for hundreds of nanoseconds This is often surprising to people new to the field who expect the power of computers to be able to accomplish much more however the sheer number of interactions that need to be calculated is staggering Methods have been developed that effectively reduce the size speed scaling to N from N however this still means that we are dependent on computational power or the use of clever methods which will be discussed later The fact that molecular dynamics MD is limited in the system sizes it models we use a simulation box also called a simulation cell on a fixed number
10. for lab members is eye strain caused by long periods of looking at computer monitor screens A list of tips to prevent eye strain from the Mayo Clinic is provided at http www mayoclinic com health eyestrain DS01084 DSECTIONS Sprevention 34 10 3 Other Safety Resources The UTD Environmental Health and Safety department http www utdallas edu ehs pro vides many resources to learn about general and work safety A couple of resources can be downloaded from ewww utdallas edu audit compliance training WorkplaceSafety pdf ewww utdallas edu ehs manuals docs occupationalandgeneralsafety pdf 35
11. is a free tool used to create high quality 3 D graphics It has been used much in the lab to generate publication quality images some of which have even made book covers POV Ray is quite powerful but is not a GUI program It is a code interpreter i e you write POV Ray code and then compile the code to generate images To compile POV Ray code from the terminal use the 21 povray filename pov command To learn more access sample images downloads POV Ray commands and tutorial links visit the POV Ray site atht tp www povray org 6 3 GIMP File Edit Select View Image Layer Colours Tools Filters Windows Help E ri AO gt DEt Ive SDE ne X 2 Hardness 050 51 x 51 ye lt I tsarineccosol 12 Y E aug A pv asx M Layer 580 6 MB Figure 8 Screenshot of open GIMP window displaying a GIMP genrated image The GNU Image Manipulation Program or GIMP is a free GUI software for image creation and manipu lation It is essentially the open source equivalent to Adobe s Photoshop GIMP can be quite useful for transforming image file types adding content to images or extracting pictures from screen shots and more GIMP features a large number of drawing tools and supports multi layering of images GIMP can typically be accessed through the panel by Applications Graphics gt GNU Image Manipulation Program or can be started from the terminal by typing the gimp command To learn more about
12. machines such as piggy bert etc If you want to access the lab computers or file system from a remote Windows machine it is helpful to use a terminal emulator A free and easy to use terminal emulator for Windows systems is PuTTY http www putty org Otherwise the system should be accessible through the Windows remote desktop logging utility 2 4 Text Editors Most of the configuration files and initial coordinate files of simulations are stored in text files Scripts program source codes and data output files are also typically stored in text files To modify or create these types of files you will need to use a text editor The choice of editor is personal preference some options are given below e Vim e GEdit e Emacs From this list Vim is a terminal program and editing text is very quick but VIM does not allow the use of the mouse to move the cursor Vim is very powerful but cryptic The shortcuts which quicken and simplify life need to be learnt and so typically has the largest initial learning curve Vim is standard to many linux distributions and can be launched by typing vi in the terminal To learn more about Vim visit the Vim website ht tp www vim org Gedit is the gnome linux equivalent of windows Word pad Gedit is typically the easiest to use and get started with It is considered to be the least powerful of the listed editors However Gedit does allow syntax coloring bracket matching line numbering etc
13. of atoms To avoid the problems associated surfaces the convention of periodic boundaries are often used where there are copies of the simulation cell around it such that an atom moving out of the cell re appears on the other side This has the effect of not having surfaces on the cell edge which is essential if the system simulated is meant to model a system from a extended environment e g a solution or cell membrane etc Furthermore MD techniques have been developed such that we can study systems in different condi tions For an isolated system the energy of the system is conserved through Newtonian mechanics and this ensemble is conceptually the easiest to treat the NV E ensemble constant number of particles constant volume constant energy However by coupling the particles in the simulation cell to a heat bath we can 30 introduce a constant temperature and study systems in NVT ensemble Here the energy of the system can change but the temperature remains constant over long periods of time The NPT ensembly constant composition pressure and temperature can be implemented by also allowing the size of the simulation cell to vary to maintain the proper pressure within the system For many chemical system which are in atmospheric pressure or within the pressure of the body this is NPT ensemble or the isothermal isobaric ensemble is the one we wish to carry out simulations on 9 Coordinate Files Coordinate files are
14. used to store static snapshots of molecular systems These files include the positions of all atoms and may include information about the types of atoms There are various types and formats of coordinate files that exist Here we will cover the two most common for use within the lab These are the PDB and XYZ format files 9 1 PDB The PDB file format stands for Protein DataBase and is probably the most widely used file format to save spatial coordinates of systems especially for biological molecules The Protein Data Bank http www pdb org pdb home home do keeps a repository of a large number of proteins which have been resolved through xray crystallography and other means A PDB file is also stored as text and therefore easily editable by hand which is a major advantage Below is a snippet from such a file Example 12345678901234567890123456789012345678901234567890123456789012345678901234567890 ATOM 145 N VAL A 25 32 433 16 336 57 540 1 00 11 92 Al N 31 ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM 146 CA VAL A 25 31 132 16 439 147 VAL A 25 30 447 15 105 148 O VAL A 25 29 320 15 059 149 CB AVAL A 25 30 389 17 437 150 CB BVAL A 25 30 166 17 399 151 CGIAVAL A 25 28 870 17 401 152 CGIBVAL A 25 30 805 18 788 154 CG2BVAL A 25 29 909 16 996 where the column and the data type are as follows 1 6 Record name ATOM 7 11 Integer Atom serial number 13
15. 16 Atom Atom name 17 Character Alternate location indicator 18 20 Residue name Residue name 22 Character Chain identifier 23 26 Integer Residue sequence number 27 AChar Code for insertion of residues 31 38 Real 8 3 Orthogonal coordinates for X in Angstroms 39 46 Real 8 3 Orthogonal coordinates for Y in Angstroms 32 58 58 II FY ST 57 57 J5 363 174 230 3 13 336 449 922 00 00 00 28 She 28 Mi T2 185 34 65 88 41 64 11 ZO 47 54 Real 8 3 Orthogonal coordinates for Z in Angstroms 55 60 Real 6 2 Occupancy 61 66 Real 6 2 Temperature factor Default 0 0 73 76 LString 4 Segment identifier left justified e 77 78 LString 2 Element symbol right justified 79 80 LString 2 Charge on the atom more information of all the types of entries in pdb files can be found at http deposit rcsb org adit docs pdb_atom_format html 9 2 XYZ The XYZ type coordinate format is one of the simplest formats and is often used for homegrown code outputs due to ease The format follows N comment line type x y z type x y z where N is the total number of atoms The comment line can be any text Example 13 particles 7 E 10 3301 13 0 430075494380179 1 373428295207335 2 226047612914703 13 0 849657136368228 0 151548730880504 1 8389481444972
16. 42 13 0 501428449094033 1 199095805189036 2 186086547932692 33 13 0 752983275021844 1 119587984733615 0 633645281498183 13 1 520445534887691 1 100300399013814 0 515246574782138 13 0 758705888807712 1 042307524638539 1 654059109324302 13 0 199673872848771 1 180678018594173 1 301612000610540 10 Lab Safety The Nielsen Lab is not a conventional wet chemistry lab and so does not follow the typical wet laboratory safety rules However the lab has its own safety concerns These can be loosely categorized into two types Equipment Safety and Personal Safety 10 1 Equipment Safety Lab members should take care when working with electronic equipment in the lab This includes but is not limited to power chord and socket safety Lab members should make sure all power chords are safely secured such as to prevent tripping Also lab members should take care not to overload power sockets and power strips as this could cause electrical shorting and may lead to electrical fire Lab members should also take care when eating or drinking near the lab equipment so as to avoid spilling these on keyboards mice etc 10 2 Personal Safety Personal safety includes awareness of things such as posture and ergonomic practices when working at the computer A list of ergonomic tips from The UTD Environmental Health and Safety office can be down loaded fromhttp www utdallas edu ehs manuals docs tips paf Another safety con cern
17. D has a site license and Mathematica can be used from the lab computers To start Mathematica simply use the command mathematica in the terminal Mathemat ica is also available on the computers at the campus library and computing labs It can also be purchased at a discounted price from the campus bookstore To learn more about Mathematica see the website at http www wolfram com mathematica 24 6 6 MATLAB fp W ARO ANDY AO NAKA AX RYAN YX AN ANN ASRS AXE ARN ON RU Yas SYR CAMRY WAN AN AN pnyyy V XXX ON Longitude NON y K Y Latitude 30 40 40 1 Figure 11 Plot generated using MATLAB MATLAB is another powerful technical computing platform that can be used for numerical computa MathWorks and like Mathematica is tion visualization and programming MATLAB is developed by However UTD has a site license for MATLAB as well and a commercial software that is not free To start MATLAB simply type and execute the matlab com it can be used on the lab computers mand in the terminal MATLAB is also available on all the campus supported computers and can be pur chased at discounted price from the campus bookstore To learn more about MATLAB visit the website at http www mathworks com products matlab 25 6 7 Office Suite The computers in the lab also carry implementations of a free open source office suite The implementation may v
18. LAMMPS and NAMD Another simulation program that can perform MD named MPDyn is also available for lab use Although use of MPDyn in the lab has declined over the past few years it is still a powerful simulator and worth mentioning 3 1 LAMMPS Tea om s a rr Figure 1 Image of AFM tip surface deformation simulation run using LAMMPS LAMMPS stands for Large scale Atomic Molecular Massively Parallel Simulator It is a classical MD code originally developed by and now distributed by Sandia National Labs LAMMPS contains a large variety of 13 functionality and is open source so can be extended by the user LAMMPS can be run on a single processor or in parallel using some form of message passing e g Message Passing Interface MPD LAMMPS can also be compiled with GPU accelerated functions The most current source code for LAMMPS is written in C More information about LAMMPS including links to the user manual tutorials a full list of standard LAMMPS commands and more can be found at the LAMMPS web site http lammps sandia gov 14 3 2 NAMD e gt Na res GE Van bad O Pa BL ote Lea neu oC St f E eE Figure 2 Image from simulation of osmotic water transport through CNTs embedded in a membrane run with NAMD NAMD is the acronym for Not just Another Molecular Dynamics simulation package NAMD has been developed namely for use in simulating large bio molecular systems or systems with
19. Unofficial Nielsen Lab Manual January 21 2015 Contents 1 Introduction 3 2 Computational Resources 3 AL EM be eck ek Ae a Bet od ots da a hn oh a A EO ee ek ee tt od oe le ct he a 3 ze OUT LAR ocacion A bale ao dk wile ele MAS a Wd a we Pe i ae dks 3 29 Environment de nb ae ee ee dh ew eed eee ee Oe WG God es 4 23 1 Logging On InLab o o oo ceca oca ee es 4 2 3 2 Terminal Working from Command Line o oo e 4 Zas Terminal Commands o n d ee io a O a cad a da 5 Zad RemoteLogging o A ae al as da 8 ZA TA Baer co coscinzsrs ara aa a ad aaa a a 10 ZA VIUSAES che a eR PRR oa ea eee ee edb 11 2 5 Launching Jobs on bigbird The Job Queue System 200 12 25 1 Current Job QUEME System io coco coc ee a a 12 3 Simulation Codes 13 Sal LAWMES aid Be A Ge de a AA U 13 ee NAND a Se oe ee SG e alao a Ee Ok SR Oe Stee at a ae Se e 15 33 AO o a ho ue hs a ew ee ee ee a eh ee ee ae 16 3 4 Other Simulation Codes gc ce ee ks crer ee ER eR da aa Ee ES 17 4 Molecular Modeling Codes 17 A YMD 6g ded de hk eee bale a ed eee ds 18 5 Plotting Software 19 ad ds AA i e ha Oe Bo ee OE eee ee ee Oe we Soe 19 a AMA de Ge he ee eee eS Be oe ee SO Se ed A 20 6 10 Other Useful Programs Applications and Tools 20 Gol PUES ss Sree ad ee he ee aS A a Sl a a i 21 G2 POV Ray orien ee bt ia ba ek eee ad ee ee ee oe ee oe ete 21 Es GIMP 2202 24540468 ba a ba dk Gi nde cacgGadahaced bake as 22 GA UME
20. ary depending on the machine but should either be OpenOffice or LibreOffice These office suites contain a word processor spreadsheet editor powerpoint editor and database editor The environment of these programs is very similar to that of implementations of Microsoft Office To access these you can go through the navigation panel e g Applications Office LibreOffice Writer The office suites can also be launched from the terminal using either openoffice org or libreoffice commands To learn more visit the websites for LibreOffice ht tp www libreoffice org and OpenOffice ht tp www openoffice org 7 Programming Languages and Resources Work in the lab often requires members to write pieces of code whether it is an analysis script for VMD a file manipulation script or a full fledged program There are many different programming languages that each have their strengths and weaknesses The languages that are currently most commonly used in the lab are Tcl Bash C Python Fortran Tcl and Bash are higher level programming languages which are typically used for scripting while C is a lower level language used for writing longer and more powerful programs Python has features allowing it to be used for both scripting and more powerful programs Fortran is a powerful language for scientific applications It is a somewhat older language and isn t used as much by lab members but is the preferred programming la
21. cl Python commands The scripting interface allows users to write their own functions and small programs to run within VMD to do all sorts of various tasks As mentioned scripting in VMD can be used for many things but is probably most commonly used within the lab for analysis of simulation systems and trajectories For more information path to downloads links to tutorials and more visit the VMD web page at http www ks uiuc edu Research vmd 5 Plotting Software Data generated in the lab often requires some form work up such as further processing etc but a crucial application is plotting data to generate charts graphs figures etc The two main graphing applications used in the lab are gnuplot and xmgrace 5 1 Gnuplot 150 100 50 1 0 40 5 0 0 0 5 1 0 Figure 5 Plot generated using Gnuplot Gnuplot is a command line graphing utility It is typically run in a terminal and can be started by typing the gnuplot command Gnuplot is capable of generating both 2 D and 3 D plots It s command line style makes for quick use and is often used in the lab to examine data on the fly although Gnuplot is capable of generating publication quality figures In the lab Gnuplot is the primary progam used to generate 3 D plots and quick 2 D plots To find out more about Gnuplot visit the website at http www gnuplot info 19 5 2 Xmgrace NP PMF for radius 5 particle T T T T T T T T T T
22. e ter minal and can also be written into scripting files It allows for the manipulation of files data launch ing of programs launching of simulations etc Bash scripting can be used to make many things much more efficient e g extracting a single line from a set of data files and parsing into a single file Lab members are highly encouraged to become familiar with Bash scripting For some more resources regard ing Bash see the sites at http www gnu org software bash manual bashref html and http www tldp org LDP abs html 713 C C is a low level object oriented programming language used to write many large and powerful pro grams e g VMD and LAMMPS are written in C C is a superset although not necessarily a strict superset of the C programming language Although there are many options for choosing a pri mary programming language C is a widely used and powerful language and is the recommended choice of programming language for lab members to learn An excellent C resource can be found at 27 http www cplusplus com 7 4 Python Python is an interpreted language Python has many features and libraries which make it usesful for both high level scripting or lower level programming Due to its relative ease of use and growing popularity it is a good introductory programming language Many useful resources for Python can be found at https www python org 7 5 Fortran Fortran is powerful low level p
23. ek kk awa E ede ee eae ee Re eee OS 23 6 5 Mathematica ooo EHS e a a ae ew oO 24 OG MATLAB oscila ee ee Ba ard eA we ee Ged 25 GT ONCE SUNS os seai a oe ew a a he Hee a aw Ge ai ew Y 26 Programming Languages and Resources 26 A Mi a we ee ee ee el oe OS ee ee a oe edd 27 oe WE ee ee a Ae eee ae ee SE a A A 27 Soe MO e Ada oe eee ee eb ee A ale ae E Ses Ge ee 27 EN TEMO on ee ee a BG 2G dS Be BS eee ee eo SOR Sw od Mee 28 Ro POW 626 2 64 Gee behead ead bbe teed aed ae ew eee eS 28 E Me a ee a Mae AA 28 Simulation Techniques 29 1 Molecular Dynamics oa ea e a edo a ee eae 29 Coordinate Files 31 OM WR ge es ead ws a ah Bowe Bk a ae hte te ge gcd a a AE a a a e e Y 31 Wi AYE oe ek ee a ae Rk ee mE ee ee 33 Lab Safety 34 10 1 Equipment Sate o ns ee ae ee A ee a a et 34 10 2 Personal SIE ob ee ae a aa a ee ee a ee ae ew 34 10 3 Other Safety Resources 0 ss e cro Pd ee we ee ee ae Oe a 35 1 Introduction Hello and welcome to the Nielsen Lab Our research group is a part of the Chemistry Department in the University of Texas at Dallas and specifically we are located at BE 3 304 in the Berkner building We are theoretical and computational group and as such the strongest chemical you will find in the Nielsen lab is coffee This is an unofficial lab manual intended to act as an introduction and reference to computational chemistry software and techniques It is ever changing and being updated so if you feel something is missing don
24. here you can type things in Once you have finished typing or editing you can exit by going back into the Command Mode by pressing lt ESC gt and then save and exit using lt SHIFT gt zz As in most of the Linux environments you can copy paste by highlighting using the mouse and and then pressing down on the scroll wheel of the mouse or the left and right mouse buttons together at the target position A word of caution VI must be in Insert Mode to paste text otherwise it will execute commands correspond ing to the pasted text which may have undesired results VI is extremely powerful and can replace text search for strings and promote world peace if you learn the commands A useful PDF cheat sheet is at http www atmos albany edu deas atmclasses atm350 vi_cheat_sheet pdf A few useful commands are given below as well 11 Command Result q Quit without saving changes u Undo last command dw Delete word 9 dd Delete 9 lines Any number of lines is allowed 9 Move cursor to line number 9 Any line number is allowed lt SHIFT gt g Move cursor to last line in file PsPpapple pear g Replaces all occurrences of text apple with pear in the file 2 5 Launching Jobs on bigbird The Job Queue System To launch large jobs or jobs with many simulations on the cluster bigbird it is useful to send the jobs through the job queue system The job queue system manages the computing resources on the clu
25. just the beginning and the end of the file If you happened to use cat on a binary file and your terminal displays funny characters afterwards you can restore it with the command reset tar zxvf lt filename tar gz gt tape archiver Untar a tarred and compressed tarball tar gz or tgz that you downloaded from the Internet Continued on next page Table 3 continued from previous page top Keep listing the currently running processes sorted by cpu usage top users first In KDE you can get GUI based Ktop from K menu under System Task Manager or by executing ktop in an X terminal ps print status Display the list of currently running processes with their process IDs PID numbers Use ps axu to see all processes currently running on your system also those of other users or without a controlling terminal each with the name of the owner Use top to keep listing the processes currently running kill PID Force a process shutdown First determine the PID of the process to kill using ps 2 3 4 Remote Logging Often you will want to use bigbird to run programs simulations etc You can log onto bigbird using the terminal Once the terminal is opened you should see your username John for example logged onto animal jbs072000 animal At this point you can log onto bigbird by entering the following command into the terminal
26. large numbers of atoms NAMD is capable of running massively in parallel or on single processors NAMD contains a lot of built in functionality written using a Charmm programming model NAMD has been developed jointly by the Theoretical and Computational Biophysics Group TCB and the Parallel Programming Laboratory PPL at the University of Illinois at Urbana Champaign and is currently distributed by the TCB NAMD is free to 15 download and is open source Although to download NAMD you must create an account with the TCB and agree to the licensing terms Links to more information and resources can be found at the TCB s NAMD web page http www ks uiuc edu Research namd 3 3 MPDyn Figure 3 Image from simulation of PEG functionalized nanoparticles at an oil water interface run using MPDyn MPDyn assumedly Molecular Particle Dynamics although this is just a guess is a simulation program developed by Watura Shinoda out of the Nanosystem Research Institute at the National Institute of Ad vanced Industrial Science and Technology AIST in Japan Dr Shinoda is a personal friend and long time collaborator of Dr Nielsen s MPDyn has been devoloped primarily for macro molecular systems 16 e g biological membranes MPDyn can do standard Molecular Dynamics simulations but can also do other simulation methods including Hybrid Monte Carlo Dissipative Particle Dynamics Path Integral Molecular Dynamics and Centroid Molecular Dy
27. lone is an equivalent of the command cd dot Current directory For example myprogram will attempt to execute the file myprogram located in your current working di rectory two dots Directory parent to the current one For example the command cd will change my current working directory one one level up Table 3 Terminal Usage Commands Command Action Usage pwd Print working directory 1 e display the name of my current di rectory on the screen df h disk free Print disk info about all the file systems in human readable form du bh more disk usage Print detailed disk usage for each sub directory starting at the root directory in human legible form Is List the content of the current directory Under Linux the com mand dir is an alias to Is Many users have Is to be an alias to 1s color cd lt directory gt Change directory Using cd without the directory name will take you to your home directory cd gt will take you to your previous directory and is a convenient way to toggle between two directories cd will take you one directory up cp lt sourcedestination gt Copy files E g cp home stan existingfilename gt will copy a file to my current working directory Use the r option for recursive to copy the contents of whole directories e g cp r myexisting dir
28. namics The MPDyn homepage is located at https staff aist go jp w shinoda MPDyn 3 4 Other Simulation Codes LAMMPS NAMD and MPDyn are the most commonly used MD programs in the lab but there are many other simulation packages available that may be encountered Just a few are listed below e CHARMM Molecular Dynamics http www charmm org e Amber Molecular Dynamics http ambermd org e xplor nih Structure Determination http nmr cit nih gov xplor nih e Jaguar Ab Initio Electronic Structures http www schrodinger com productpage 14 7 Of course the above is by no means a comprehensive list There are a myriad of simulation codes that use various methods and often are geared for specific applications However a much more comprehensive list of Molecular Mechanics and Molecular Modeling software is available at the Wikipedia page atht tp en wikipedia org wiki List_of_software_for_molecular_mechanics_modeling 4 Molecular Modeling Codes Molecular Modeling Code may seem like another good name for simulation codes but to differentiate a molecular modeling code is software in which the predominate function is visualization i e these types of software are used to look at build and often analyze the structures e g molecules atom configurations or any other simulated system that are used generated in simulations Molecular modeling codes are very use ful and are often quite powerful usually
29. nguage of Dr Nielsen Therefore it is useful to at least become familiar enough to be able to read and make small modifications to Fortran code Additional information and links to resources are given in the following subsections for theses languages However there are many many languages that can be used Some additional choices could be C C Ruby etc A more comprehensive list of programming languages is given on this Wiki page http en wikipedia org wiki List_of_programming_languages 26 7 1 Tel Tcl or Tool Command Language is higher level programming language It is often used as an embedded scripting interface in large programs through the use of the Tk console but is not limited to such applica tions VMD uses Tcl and the Tk console as the primary scripting interface It is highly recommended that lab members become familiar with using Tcl for scripting in VMD although VMD does offer a Python interpreter making Python a viable alternative Tcl in VMD scripting Some more information can be found at the following sites http tcl sourceforge net and http www tcl tk The VMD user guide has a large section that covers scripting in VMD which can be referenced for learning VMD specific functions and examples The download links to the user guide for VMD can be found at http www ks uiuc edu Research vmd current docs html 7 2 Bash Bash or the Bourne Again Shell is a free Unix shell Bash serves as a command processor from th
30. ograms 2 3 3 Terminal Commands The terminal is an input output source where you can type in commands and display information The more used to the system you become the more you start using the terminal as it allows quick access commands to manipulate files directories and also show information The complete list of Linux terminal commands can be found at http ss64 com bash Usually only a handful of commands are needed to start working on a terminal and a list of the most commonly used ones are given below from http www unixguide net linux linuxshortcuts shtml Table 2 Terminal Usage Shortcuts lt Tab gt In a text terminal Auto complete the command if there is only one option or else show all the available options THIS SHORT CUT IS GREAT It even works at LILO prompt lt gt Scroll and edit the command history Press lt Enter gt to exe cute previous commands lt Ctrl gt c Kill the current process mostly in the text mode for small appli cations lt Ctrl gt z Send the current process to the background lt MiddleMouseButton gt Paste the text which is currently highlighted somewhere else This is the normal copy and paste operation in Linux tilde My home directory normally the directory nome myloginname For example the command cd mydir will change my working directory to the subdirectory myditr under my home directory Typing just cd a
31. rogramming language that was developed especially for numerical and sci entific computing Although originally developed in the 1950s Fortran remains widely in use for numer ically intensive computations One source of information and tutorials can be found at http www fortran com the fortran company homepage fortran tutorials 7 6 LaTeX LaTeX is free document preparation system with many features designed for technical and scientific writing It is quite powerful and includes many features which make scientific writing much cleaner and often much easier It is thus commonly used in the lab for writing articles book chapters etc e g The source for this manual was written in LaTeX LaTeX is a programming style language i e the user writes code in LaTeX which is then compiled to generate the actual document e g with pdflatex section 6 1 to generate a pdf document To learn more about LaTeX see the website at http www latex project org 28 8 Simulation Techniques 8 1 Molecular Dynamics Molecular dynamics is a computer simulation method where we study the movement of atoms and molecules Conventionally this is classical mechanics method i e we do not use quantum mechanics where the force acting on each atom is calculated through the application of Newtons laws The instantaneous force and hence the resulting velocities of the atoms are computed and through using time integrator the atoms are moved accordingly over a
32. so any self compiled programs should run on any machine in the lab Before being able to log into the network you need to fill in some paperwork for UTD to create an account which usually takes several weeks or even months sometimes During this time you will most likely use another lab member s account If this is the case then your host will need to log in for you to have access to lab machines 2 3 1 Logging On In Lab If the machine is off just turning it on will after a good 15 minutes some times take you to a log in screen Your username will usually be your netid After entering the userid enter your password to log into the NSM system All the machines in the lab work on this system and every machine will log into your home directory in the NSM network For example a user John B Smith with a user id of jbs072000 will have a home directory located on the NSM network net uu nm cm jbs07 1000 Once logged onto the machine you can use Linux much like any windows machine 2 3 2 Terminal Working from Command Line You will often run commands from the terminal The terminal is just a place where you can type in com mands and display some information The terminal usually can be started from the system tools using Panel Applications gt System Tools Terminal The terminal will allow you to do things such as navigate through your directories folders display file contents move copy data files and execute pr
33. ster and allows jobs to be lined up queued and run automatically when the appropriate numbers of CPUs become available 2 5 1 Current Job Queue System The job queue system that is currently on bigbird is SLURM https computing 1linl gov linux slurm SLURM stands for Simple Linux Utility for Resource Management and is an open source resource management system The most useful and basic commands will be covered here but more extensive resources can be found in the SLURM documentation at https computing 1linl gov linux slurm documentation html The most basic command to launch jobs is the srun command Example srun job_binary There are also command line options and flags that can be used when launching jobs with SLURM The three basic resource request flags are given in the Table 4 Once jobs have been submitted you can check the queue status with command squeue squeue will list all jobs that have been submitted to the queue system along with useful information about the job s status 12 Flag Use N Number of nodes requested n number of tasks to run on each node C number of cpus per task Table 4 An example use of srun with the flags is srun N1 n1 c8 job_binary where the job is sent into the queue requesting that one node be used with one task and eight CPUs for that task 3 Simulation Codes There a couple of MD simulation programs that are most often used in the lab These include
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