PINY MD Manual: - Data to Insight Center
Contents
1. num_proc_tot 1 If running the code on a parallel platform this keyword must be set to the total number of processors requested num_proc_class_forc 1 If running a classical MD calculation on a parallel platform this keyword must be set to the number of processors requested for classical force level parallelization num_proc_beads 1 If running a path integral calculation on a parallel platform this keyword must be set to the number of processors requested for path integral bead level parallelization num_proc states 1 If running a Car Parrinello calculation on a paralle platform this keyword must be set to the number of processors requested for state or reciprocal space level parallelization see cp_para_typ keyword in sim_cp def section min_num_atoms_per_proc O In classical parallelization using the Plimpton force decomposition algo rithm specify the minimum number of atoms on a processor num_proc_class_forc_src O In classical parallelization using the Plimpton force decomposition algo rithm the keyword must be specified according to the number of source processors requested num_proc_class_forc_trg 0 In classical parallelization using the Plimpton force decomposition algo rithm the keyword must be specified according to the number of target processors requested rndm_seed 19541 Specify a seed for the random number generator 24 generic_fit_opt off on For2. cp_nhe_tau_def 25 Time scale in femtoseconds on which the coefficient thermostats should evolve cp nhe_len 3 Length of the coefficient thermostat chain cp_respa_steps_nhc 2 Number of individual Suzuki Yoshida factorizations to be employed in 13 11 12 13 14 integration of the coefficient thermostat variables Only increase if energy conservation not satisfactory with default value Nep yosh steps nhc 3 Order of the Suzuki Yoshida integration scheme for the coefficient thermo stat variables Only increase if energy conservation not satisfactory with default value init_rescale_cp_nhc off on Initially rescale coefficient thermostat velocities according preset fictitious electron kinetic energy cp_heat_therm_fact 1 0 Heat the coefficient thermostats by a an amount equal to the preset ficti tious electron kinetic energy times the factor in curly brackets This helps maintain adiabaticity in the thermostat variables thermostat_type 1 1 NHC 2 CGMT Choose a thermostatting type either Nos Hoover chain thermostatting NHC or generalized Gaussian moment thermostatting GGMT 14 sim write def 29 keywords 10 write_screen_freq 1 Output information to screen will be written with a frequency specified in curly brackets Write dump freq 1 The restart file of atomic coordinates and velocities etc will be written with a frequency specified in cur
3. A diagonal approximation to the electronic Hessian is used for wave func tion minimization as a preconditioner The Hessian elements are Hgg Ig 2 Vag where g is the reciprocal space vector In the brackets you specify at what energy to cutoff this diagonal approximation and use a constant diagonal hessian If a given minimization run is not converging well try increasing this value 26 sim pimd def 11 keywords 1 path_int_beads 1 Number of path integral beads 2 path_int_md_typ staging centroid Path integral molecular dynamics type staging or centroid normal mode This defines the variable transformation type to be used Staging gives the fastest equilibration however centroid allows centroid MD to be per formed One of the two options MUST be used i e it is NOT possible to performe path integral MD calculations without one of these variable transformations 3 pathint_gamma_adb 1 Path integral molecular dynamics type adiabaticity parameter Employed with the centroid option to give approx to quantum dynamics The mode masses are divided by the factor in curly brackets Hence the number must be greater than 1 4 respa_steps_pimd 1 Number of RESPA steps to use for the harmonic part of the path integral action 5 Ninitial spread size 1 In growing cyclic initial paths what is the how large do you want their diameter or spread in Angstroms 6 Ninitial spread opt on off Do you wan
4. of system in atmospheres Only used for simulations in the NPT ensembles surf_tens O External surface tension in Newtons meter for constant surface tension calculation gen_alpha_clus 7 When using reciprocal space cluster wire or surface boundary conditions method this keyword is set to the convergence parameter used in the subdivision of the Coulomb potential 1 r erf ousr r erfe acusr r This parameter is dimensionless The actual value of a is the value specified divided by the cube root of the volume gen_ecut_clus 20 When using reciprocal space cluster bondary conditions method this key word specifies the plane wave basis set kinetic energy cutoff for generating a FFT grid that will be used to compute the Fourier coefficients of the long range potential component erf aq r r The grid should be finer than that used for performing any other FF Ts in the calculation If it is set too low the code will automatically set it to 1096 higher than the specified cutoff for the actual plane wave basis set annealing_opt on off Perform an annealing run on annealing_start_temperature 0 1 Take the initial temperature to be the number in brackets 6 14 15 16 17 18 19 20 21 22 23 annealing target temperature 300 0 Stop the annealing run when the number in brackets is reached annealing rate 1 0 Scale velocities by the number in brackets at each step
5. or lowdin cp_check_perd_size on off In ab initio MD simulations of clusters wires and surfaces option to check inter particle distances to see if particles have escaped the box cp_tol_edge_dist 3 In ab initio MD simulations of clusters wires and surfaces option to check cluster size vs box size to make sure chosen box size is large enough cp_dual_grid_opt off not prop not_prop stands for not proportional and should be used to turn on the dual grid use Careful proportional is not debugged cp check_dual_size on off Check cluster size under the dual grid option 24 22 23 24 25 26 27 28 29 30 31 32 33 cp_energy_cut_dual_grid_def 2 Plane Wave Cutoff on big grid or long range part of the energy Accepted range 2 20 cp alpha_conv_dual 7 Parameter to divide the energy into short range long range The larger it gets more of the energy is taken to be long range Accepted range 6 10 inter_pme_dual 4 an even number The method works by interpolating the density on the small grid onto the large grid This parameter is the order of the interpolation cp sic off on Use self interaction corrected DFT This option is not implemented cp_gauss off on Enforce the orthogonality constraints via Gauss principle of least con straint This option is not implemented cp_nl_list off on Determine nonlocal interactions via a list r
6. typ md minimize debug Perform one of the following types of simulations md Force field based classical molecular dynamics minimize Force field based classical minimization cp Car Parrinello based ab initio molecular dynamics cp min Ab initio minimization cp_wave_min Single point wavefunction minimization pimd Force field based path integral molecular dynamics cp_pimd Ab initio path integrals cp_wave_min_pimd Single path wavefunction minimization debug Force field debug option for developers only debug cp Ab initio MD debug option for developers only 3 ensemble_typ nve nvt npti npt_fnst Use the statistical ensemble specified in the curly brackets npt i and npt f refer to isotropic and flexible cell constant pressure and nsf refers to con stant surface tension 4 Nminimize typ min std min cg min diis Perform a minimization run using the method specified in curly brackets min_std Steepest descent min cg Conjugate gradient 10 11 12 13 min diis Direct inversion in the iterative subspace num_time_step 0 Total number of time steps for this run time_step 1 Fundamental or smallest time step in femtoseconds If no multiple time step integration is used then this is the time step temperature 300 Atomic temperature in Kelvin This is the temperature used for velocity rescaling velocity resampling thermostatting etc Vpressure 0 Pressure
7. which the histogram is printed 35 data base def 1 interfile File containing intermolecular interaction parameters 2 vps_file pimd inter File containing pseudopotential interaction parameters 3 bond_file pimd bond File containing bond interaction parameters 4 bend_file pimd bend File containing bend interaction parameters 5 tors_file pimd tors File containing torsion interaction parameters 6 onefour_file piimd onfo File containing onefour interaction parameters 36 Topology Keyword Dictionary The following commands maybe specified in the molecular topology and parameter files 1 molecule name def 2 residue def 3 residue bond def 4 residue name def 5 atom def 6 bond def 7 grp bond def 8 9 bend def bend bnd def 10 tors def 11 onfo def 12 residue morph 13 atom destroy 14 atom create 15 atom morph 37 molecule name def 1 molecule name Molecule name in characters 2 nresidue Number of residues in the molecule 3 natom Number of atoms in the molecule 38 residue def 1 Nesidue name Residue name in characters 2 residue_index Residue index number this is the third residue in the molecule 3 natom Number of atoms in the residue after morphing 4 residue_parm_file Residue pa
8. 0 Time scale of volume heat bath evolution under constant pressure in fem toseconds 3 periodicity 0 1 2 3 0_ewald 0 for cluster 1 for wire 2 for surface 3 for solid 4 intra_perds off on Use periodic imaging for the intramolecular interactions Important when using periodicity to elongate molecules such as polymers 22 sim cp def 37 keywords 1 Nep restart type gen wave restart pos restart posvel restart all Keyword to specify how the coefficients in a Car Parrinello run should be initialized gen wave Start from atomic orbitals and perform a wave function optimization restart pos Read in optimized coefficients or coefficients from a previous run restart posvel Read in coefficients and coefficient velocities restart all Read in coefficients coefficients velocities and coeffi cient thermostats 2 cp_para_typ hybrid full_g Parallelize the g vectors or use a hybrid state g vector scheme 3 NVcp dft typ 1da lsda gga 1da gga 1sda Type of local approximation to density functional theory 4 cp_vxc_typ pztIRda pw_Ida pz_tsda LDA LSDA exchange correlation functional If the Lee Yang Parr GGA correlation functional is specified only the exchange part of the specified functional is used 5 Ncp ggax typ becke pbe x revpbe x rpbe x xpbe x brx89 brx2k pw91 GGA exchange functional desired 6 cp_ggac_typ lyp lypm1 xpbe_c pbe_c taul_c pw91c off GGA correlation fun
9. PINY_MD Manual Modern Simulation Methods Applied to Chemistry Glenn J Martyna Physical Sciences Division IBM T J Watson Lab P O Box 218 Yorktown Heights NY 10598 Mark E Tuckerman Dept of Chemistry and Courant Institute of Mathematical Sciences New York University New York NY 10003 Introduction There are four types of files from which the PINY_MD script language interface reads commands the simulation setup file the system setup file molecular parameter topology files and potential energy parameter files Coordinate input files do not contain commands but simply free format data In the simulation setup files commands that drive a given simulation are stated For example run 300 time steps of Car Parrinello path integral molecular dynamics parallelized over 15 processors 5 for the beads and 3 for each of the 5 densities In the system setup file the system is decribed For example 300 water molecules two peptides three counter ions thirty Kohn Sham states etc Topology files contain in formation about the molecular connectitivity optional for Car Parrinello and potential energy pseudopotential files contain information about the interactions All the commands could be placed in the same file However this is not recom mended The idea behind the file division is that one often modifies the simulation commands occationally the system setup commands but seldom the topology and po tential energy information
10. The four file types help organization and transferability For example many simulation command files can drive the same system setup file molecular parameter topology files and potential energy parameter files In order to run the code type piny md machine e sim input in where machine is the machine type and sim_input in is the input file Both names are arbitrary Note that any simulation can be stopped automatically in the directory in which it is running even if the number of cycles has not been reached by simply typing touch EXIT The code will automatically check for the existence of a file called EXIT in your directory and if found will perform on more step and then terminate writing out all quantities of interest and a restart file Finally there are three levels of grouping for the PINY MD commands meta keywords keywords and key arguments The first level the meta keywords sort keywords into nat urally connected groups The second level the keywords are specific commands to the computer program The third level key arguments are the arguments to the keywords The syntax looks like meta keywordl Nkeywordl keyargl keyword2 keyarg2 2 meta_keyword2 keywordl keyarg1 keyword2 keyarg2 The commands are case insensitive and can be specified in any order Warning The code will warn the user and stop the run if it isn t happy with the input The designers felt that not running a simulation was bet
11. art file Coefficients for next run are written to this file with a frequency equal to the dump frequency cp_restart_in_file file coef_in Name of input coefficient restart file Starting coefficients are read from this file cp_fseigs_file sim_cp_kseigs out none Name of the Kohn Sham energy eigenvalue trajectory file cp elf_file sim_cp_elf out none Name of electron localization function output file 17 sim list def 10 keywords 10 neighbor_list no_list ver_list nk list Type of neighbor list to use Optimal scheme for most systems ver_list with a Ink_Ist update type update_type Ink_Ist no_list Update the verlet list using either no list or a link list verlist_skin 1 Skin depth added to verlet list cutoff Needs to be optimized between extra neighbors added and average required update frequency brnch_root_list_opt on off If turned on then the neighbor list is updated using the branch root scheme brnch_root_list_skin 0 Skin depth added to the branch root list brnch_root _cutoff 1 112 Cutoff for branch root scheme Ink_cell_divs 7 Number of link cell divisions in each dimension Needs to be optimized if used either as list type or update type verlist_pad 30 Pad the Verlet list by the amount specified in curly brackets verlist mem_safe 1 25 Scale up the amount of memory allocated for the Verlet list by the amount in curly brackts verli
12. ather than on the fly Useful for very large systems nlvps_list_skin 50 0 If using a nonlocal list use a skin of length specified in curly brackets cp _cg_line_ min len 0 gt 3 Number of points used to do a simple line minimization with conjugate gradient cp diis_hist len 10 Number of DIIS history vectors to keep diis_hist_len 10 Number of atomic DIIS history vectors to keep zero_cp_vel no initial periodi Zero the coefficient velocities initially periodically or not at all cp_move_dual_box_opt off on Option to allow the small CP box in QM MM calculations to move This option is not yet implemented 25 34 35 36 3T Vcp elf calc frq 0 Option to calculate the electron localization function ELF with a fre quency determined by the number in curly brackets Generally this func tion is calculated only once for a single electron configuration however it is possible to accumulate an ELF trajectory if you have the disk space cp_ngrid_skip 1 Number of grid points along each direction to skip when writing out the ELF saves disk space cp_isok_opt off on Control fictitious electron kinetic energy via the isokinetic method This option is recommended for systems that are otherwise difficult to control Note that this approach is an alternative to the usual Nos Hoover chain or GGMT extended thermostatting options for the coefficients cp_hess_cut 1 5
13. ctional desired 7 Ngradient cutoff 5 0e 05 If the density is smaller than the value in curly brackets switch off the GGA functional using a switching function 8 Ncp mass tau def 25 CP fictitious dynamics time scale in femtoseconds 9 cp_mass_cut_def 2 Renormalize CP masses for E lt h g 2m Rydberg 23 10 11 12 13 14 15 16 17 18 19 20 21 cp_energy_cut_def 2 Plane wave expansion cutoff E lt hg 2m cp fict KE 1000 Fictitious electron kinetic energy in Kelvin for Car Parrinello calculations cp_e_e_interact on off Electron electron interactions can be turned off for one electron or non interacting quantum particle problems cp_norb full_ortho norm_only off Integrate the CP equations of motion in nonorthogonal orbitals see Hut ter Tuckerman and Parrinello J Chem Phys 102 859 1995 cpminimize_typ min_std min_cg min_diis Minimization type steepest descent conjugate gradient or DIIS cp_ptens on off Evaluate the pressure tensor in a Car Parrinello simulation This option is not recommended unless you really need this number or you want to do constant pressure Car Parrinello cpinit_orthog on off Orthogonalize the electronic orbitals at the start of a run Useful if you wish to change from nonorthogonal orbitals to orthogonal orbitals cp_orth_meth gram_schmidt lowdin Orthogonalize using gram schmidt
14. es in the spin down electron density 3 cp_nhc_opt none global glob st ind_st mass_coef Nose Hoover Chain coupling option The plane wave coefs are coupled to none no thermostats global a global coef thermostat glob st a thermostat for spin up coefs or spin down coefs ind st a thermostat for each state mass coef a thermostat for coef 4 Ncp tau nhc 25 Nose Hoover Chain coupling time scale 33 bond free def 10 11 12 13 atom1_moltyp_ind Index of molecule type to which atom 1 belongs atom2_moltyp_ind Index of molecule type to which atom 2 belongs atom1_molind Index of the molecule of the specified molecule type to which atom 1 be longs Natom2 mol ind Index of the molecule of the specified molecule type to which atom 2 be longs Vatoml1 residue ind Index of the residue in the molecule to which atom 1 belongs Vatom2 residue ind Index of the residue in the molecule to which atom 2 belongs atoml_atm_ind Index of the atom 1 in the residue atom2_atm_ind Index of the atom 2 in the residue eq rs Equilibrium bond length in Angstrom fk Umbrella sampling force constant in K Angstrom rmin_hist Min Histogram distance in Angstrom rmax_hist Max Histogram distance in Angstrom num_hist Number of points in the histogram 34 14 hist_file File to
15. f intermolcular forces A zero indicates intermolecular forces are updated every step shake_tol 1 0e 6 Constraints not treated by the group constraint method are iterated to a tolerance given in curly brackets rattletol 1 0e 6 Time derivative of constraints not treated by the group constraint method are iterated to a tolerance given in curly brackets max_constrnt_iter 200 Maximum number of iterations to be performed on constraints before a warning that the tolerance has not yet been reached is printed out and iteration stops 10 19 20 21 22 23 24 25 26 27 group con tol 1 0e 6 Group constraint method is iterated to a tolerance given in curly brackets min_tol 0 0002 Iterate atom minimization until the force convergence measure AF 1 2 a N DAF F is less than the number in curly brackets Here N is the number of atoms in the system cp min tol 0 0002 Iterate wave function minimization ab initio calculations only until the 1 2 force convergence measure Ay 1 Noce ye edd is less than the number in curly brackets Here Noce is the number of occupied states and y is the derivative of the energy with respect to the bra orbital cpnorb_tol 1 e 3 When running Car Parrinello calculations with nonorthogonal orbitals this keyword is used to monitor the maximum value of the off diagonal elements of the overlap matrix v v If the max
16. fferent than the ex ternal temperature for fancy simulation studies in the adiabatic limit mol_freeze_opt none all backbone Freeze this molecule to equilibrate the system hydrog_mass_opt A B Increase the mass of type A hydrogens where A is off all backbone or sidechain to B amu This allows selective deuteration for example hydrog_con_opt off all polar Constrain all bonds to this type of hydrogen in the molecule mol_nhc_opt none global glob_mol ind_mol res_mol atm_mol mass_mol Nose Hoover Chain option Couple the atoms in this molecule to none no thermostats x global the global thermostat glob mol a thermostat for this molecule type ind mol a thermostat for each molecule of this type res mol a thermostat for each residue in each molecule atm mol a thermostat for each atom in each molecule x X X X mass mol a thermostat for each degree of freedom 30 11 mol_tau_nhc Nose Hoover Chain time scale in femtoseconds for this molecule type 3l harmonic analysis 1 harmonic_frequencies on off Perform a calculation in which harmonic frequencies are computed 2 Minite difference displacement 0 001 Use the step length in brackets for computing finite differences of the forces to obtain the atomic Hessian elemenets 32 wavefunc def 1 nstate_up 1 Number of spin up states in the spin up electron density 2 nstate_dn 1 Number of spin down stat
17. g final atomic coordinates and velocities in_restart_file sim_restart in Name of the file containing initial atomic coordinates and velocities for this run instant_file sim_instant out File to which instantaneous averages are to be written Vconf partial limits 1 0 Write atomic positions only with indices between the limits specified in the curly brackets Vconf partial file sim atm pos part out Partial trajectory position file name Vatm pos file sim atm pos out Trajectory position file name Vatm vel file sim atm vel out Trajectory force file name Vatm force file sim atm force out Trajectory velocity file name Vatm force file sim atm force out none Name of atomic force trajectory file Wmol set file sim atm mol set in Name of file containing instructions on how to name and build molecules Detailed instructions on contents of this file given elsewhere screen_output_units au kcal_mol kelvin Output information is written to the screen in units specified in curly brackets Vconf file format binary formatted Trajectory files are written either in binary or formatted form 16 24 25 26 27 28 29 cp coefffile file confc Name of coefficient trajectory file read_binary_cp_coeff on off Read coefficients from a binary format coefficient restart file cp_restart_out_file file coef_out Name of output coefficient rest
18. idue morph file Uses the same key words as atom def atom morph Used to morph an atom in a residue morph file Uses the same key words as atom def 45 Potential Parameter Keyword Dictionary The following commands maybe specified in the potential parameter files inter parm bond parm bend parm onfo parm 1 2 4 tors parm y 6 pseudo parm 7 bend bnd parm 46 inter parm 10 11 12 13 atoml Atom type 1 character data atom2 Atom type 2 character data pot_type lennard jones williams aziz chen null Potential type Williams is an exponential c6 c8 c10 Aziz chen has a short range switching function on the vanderwaals part Amin dist Minimum interaction distance max_dist Spherical cutoff interaction distance res_dist Respa Spherical cutoff interaction distance sig Lennard Jones parameter eps Lennard Jones parameter c6 Wiliams Aziz Chen Vdw parameter eset ra Williams Aziz Chen Vdw parameter c9 Williams Aziz Chen Vdw parameter cl0 Williams Aziz Chen Vdw parameter Awill Williams Aziz Chen parameter Aexp Br Cr AT 14 Bwill Williams Aziz Chen parameter Aexp Br Cr 15 Cwill Williams Aziz Chen parameter Aexp Br Cr 16 rm_swit Williams Aziz Chen parame
19. imum value exceeds the number in curly brackets a unitary transformation of the orbitals that diagonalizes the overlap matrix is performed cp shak_tol 1 0e 6 The coefficient orthogonalization constraint is iterated to a tolerance spec fied in the curly brackets cp_rattle tol 1 0e 6 The time derivative of the orthogonalization constraint is iterated to a tolerance specified in the curly brackets cptrun_tol 2 0 During a Car Parrinello run monitor the coefficient force tolerance mea sure Ay If this measure exceeds value in curly brackets print out a warning message to the user in the screen output file class_mass_scale_fact 1 0 In atomic minimization calculations it is sometime useful to uniformly scale the atomic masses in order to increase the step size uniformly This keyword allows the user to have this scaling without having to edit parameter files Masses are all divided by the number in curly brackets hess_opt unit full diag In atomic minimization specify an approximate form for the atomic Hes 11 28 29 30 sian either a unit matrix a diagonal matrix or the full atomic Hessian Default is unit hmat_int_typ normal upper _triangle For NPT calculations invoke specialized integrators that use the box ma trix in normal or upper triangle form hmat_cons_typ none ortho_rhom mono clin For NPT calculation constraint the box matrix to be orthorhombic allow the lengths
20. incoming atom Atom to be bonded root atom 0 0 Ist atom bonded to root atom 1 0 2nd atom bonded to root atom 2 0 1st atom bonded to 1st branch 1 1 2nd atom bonded to 1st branch 1 2 8 def_ghost1 index coeff If the atom is a ghost these funky sites that TIP4P type models have it spatial position is constructed by taking linear combinations of the other atoms in the molecule specified by the index and the coef A ghost can be composed of up to six other atoms ghost 1 ghost 6 9 cp_atom yes no Is this atom an ab initio atom 42 10 cp_valence_up If this is an ab initio atom give the number of spin up electronic states to assign to this atom in order to build the initial wave function 11 cp_valence_dn If this is an ab initio atom give the number of spin down electronic states to assign to this atom in order to build the initial wave function 43 bond def 1 atoml1 Numerical index of atom 1 2 atom2 Numerical index of atom 2 3 modifier con on off The bond is active on inactive off or constrained con 44 residue morph Used to define a file which contains modifications to a given residue It has the same arguments as residue name _def atom destroy Used to destroy an atom in a residue morph file Uses the same key words as atom def atom create Used to create an atom in a res
21. lly The atoms po sitions then follow in the order specified by the set file and the topology files Finally at the bottom of the code the 3x3 simulation cell matrix must be specified The unit is Angstrom Example The molecular set file specifies 25 water molecules as molecule type 1 and 3 bromine atom as molecule type 2 The water parameter file is written as OHH i e oxygen is atom 1 hydrogenl is atom 2 hydrogen2 is atom 3 Therefore the input file should have 25 OHH coordinates followed 3 bromines If the box is a square 25 angstrom on edge then the last three lines of the file should be 25 00 0 250 0 0 25 51
22. ly brackets Write inst freq 1 Instantaneous averages of energy temperature pressure etc will be writ ten to the instantaneous file with a frequency specified in curly brackets write_pos_freq 100 Atomic positions will be appended to the trajectory position file with a frequency specified in curly brackets Write vel freq 100 Atomic velocities will be appended to the trajectory velocity file with a frequency specified in curly brackets Write force freq 1000000 Atomic forces are written to the trajectory force file with a frequency specified in the curly brackets Vconf partial freq 100 Append partial configuration file with a frequency specified by the number in curly brackets path_cent_freq 100 Append centroid trajectory file with a frequency specified by the number in curly brackets write_binary_cp_coeff on off Write the coefficient restart file in binary form Default if off write_cp_c_freq 100 Append the coefficient trajectory file with a frequency specified by the number in curly brackets This option should only be used if very large amounts of disk space are available or the system is very small 15 11 12 13 14 15 16 1T 18 19 20 2 22 23 sim_name sim_input out Name of file containing all keywords both user set a default out_restart_file sim_restart out Name of the restart dump file containin
23. machines without a built in FFT a generic FFT routine is provided Specify on to use this option sim run def 30 keywords 1 zero_com_vel yes no If set to yes the center of mass velocity is initially set to 0 2 init resmp_atm_vel on off If turned on atomic velocities are initially sampled resampled from a Maxwell distribution 3 resmpl_frq_atm_vel 0 Atomic velocities are resampled with a frequency equal to the number in the curly brackets A zero indicates no resampling is to be done 4 init_rescale_atm_vel on off If turned on atomic velocities are initially rescaled to preset temperature 5 rescale_frq_atm_vel 0 Atomic velocities are rescaled to desired temperature with a frequency equal to the number in the curly brackets A zero indicates no resampling is to be done 6 init_rescale_atm_nhc on off If turned on atomic thermostat velocities are initially rescaled to preset temperature 7 initresmpl_cp_vel off on When running Car Parrinello calculations this keyword allows the user to initially sample an initial set of coefficient velocities from a Maxwell Boltzmann distribution according to the preset fictitious electronic kinetic energy 8 resmpl_frq_cp_vel O When running Car Parrinello calculations this keyword allows the user to periodically resample the coefficient velocities with a frequency specified by the number in curly brackets 0 indicates no periodic resa
24. mpling 9 init_rescale_cp_vel off on When running Car Parrinello calculations this keyword allows the user to initially rescale the coefficient velocities according to the preset fictitious electronic kinetic energy 10 11 12 13 14 15 16 1T 18 init resmpl_cp_nhc off on When running Car Parrinello calculations this keyword allows the user to initially sample an initial set of set of coefficient thermostat velocities according to the preset fictitious electronic kinetic energy This option may be used only if extended system Nos Hoover chain or GGMT thermotats are turned on for the coefficient dynamics cp_ks_rot 0 Perform a periodic unitary transformation of the orbitals in a Car Parrinello run to generate the instantaneous Kohn Sham orbitals with a frequency equal to the number in curly brackets respa_steps_Irf 0 Number of short time steps to be taken between long range force updates A zero indicates long range forces are updated every step respa_rtheal 1 If respa_steps_Irf is not zero then the long range and short range forces are both switched off in space with a switching function of healing length given in the curly brackets respa_steps_torsion 0 Number of short time steps to be taken between updates of torsional forces A zero indicates torsional forces are updated every step respa_steps_intra 0 Number of short time steps to be taken between updates o
25. rameter file 5 residue_fix_file File containing morphing instructions for this residue if any 39 residue bond def 1 resl_typ Residue name in characters 2 res2_typ Residue name in characters 3 resl_index Numerical index of first residue 4 res2_index Numerical index of second residue 5 Nesl bond site Connection point of residue bond in residue 1 6 res2_bond_site Connection point of residue bond in residue 2 7 resl_bondfile Morph file for residue 1 lose a hydrogen for example 8 res2_bondfile Morph file for residue 2 lose a hydrogen atom for example 40 residue name def 1 Nes name Name of the residue in characters 2 natom Number of atoms in the residue 41 atom def 1 atom_typ Type of atom in characters 2 atomind This is the nth atom in the molecule The number is used to define bonds bends tors etc involving this atom 3 mass The mass of the atom in amu 4 charge The charge on the atom in e 5 valence The valence of the atom 6 Nimproper def 0 1 2 3 How does this atom like its improper torsion constructed if any 7 bond_site_1 site prim branch sec branch To what bond site s character string does this atom belong and where is it in the topology tree structure relative to the root the atom that will bonded to some
26. st_mem_min 2000 Specify a minimum size of list scratch length Forces will be computed in chunks of length specified in the curly brackets 18 sim class PE def 24 keywords 10 ewald_kmax 7 Maximum length of k vectors used in evaluating Ewald summation for electrostatic interactions ewald_alpha 7 Size of real space damping screening parameter in Ewald sum Actual value of a used in calculating the Ewald sum is the number in curly brack ets divided by the cube root of the volume ewald_respa_kmax 0 Maximum length of k vectors used in long range force RESPA integration ewald_pme_opt on off If turned on then electrostatic interactions are evaluated using the smooth particle mesh method Its use is recommended ewald_kmax_pme 7 Maximum length of k vectors used in evaluating Ewald summation for electrostatic interactions via the smooth particle mesh method ewald_interp_pme 4 Order of mesh interpolation in the smooth particle mesh Ewald method ewald_respa_pme_opt on off If turned on then long range force RESPA is used in conjunction with the smooth particle mesh method ewald_respa_interp_pme 4 Order of mesh interpolation in the smooth particle mesh Ewald method used with RESPA ewald_respa_kmax_pme 7 Maximum length of k vectors unsed in evaluating the Ewald sum for elec trostatic interactions with the smooth particle mesh method in conjunction with RESPA in
27. t initial paths grown for you Should only be used once per path integral calculation 7 pi beads_level_full 1 Use fully separated RESPA beads i e no potential in the bead reference system This option is not yet implemented 8 pi_beads_level_inter_short 0 Include short range intermolecular in teractions in bead reference system This option is not yet implemented 9 pi_ beads_level_intra_res O Include bonds and bends only in the bead reference system This option is not yet implemented 2r 10 pi_beads_level_intra O Include full intramolecular interaction in the bead reference system This option is not yet implemented 11 Npimd freeze type centroid all mode Freeze beads at some level either centroids only or all modes 28 Molecule and Wave function Keyword Dictionary The following commands maybe specified in the system setup file 1 molecule def 2 harmonic analysis 3 wavefunc def 4 bond free def 5 data base def 29 molecule def 10 mol_name The name of the molecule type inum mold The number of this molecule type you want in your system num_residue The number of residues in in this molecule type mol_index 2 This is the 2nd molecule type defined in the system Wnol parm file 5 The topology of the molecule type is described in this file mol_text_nhc The temperature of this molecule type It may be di
28. te this will not affect the total target pressure for the simulation pseud_spline_pts 4000 Number of points used to spline up the pseudopotentials in ab initio MD calculations scratchlength 1000 Specify a scratch length for intermolecular interactions Interactions are computed in chunks of size determined by the number in curly brackets sep_VanderWaals off on Report the Van der Waals component of the energy separately in the screen output file dielectric_opt off on 20 21 22 23 24 Approximate presence of a solvent by a distance dependent dielectric con stant dielectric_rheal 1 0 Switch off the distance dependence of the dielectric constant with a switch ing function with the healing length specified in the curly brackts dielectric_cut 1 0 Switch off the distance dependence of the dielectric constant at a distance specified in curly brackets dielectric_eps 1 0 Switch off the distance dependence of the dielectric constant to a value specified in curly brackets inter_PE_calc_freq 5 Calculate the total potential energy with a frequency specified in curly brackets The total energy is only used to evaluate energy conservation Calculating the total potential energy less frequently can save CPU time 21 sim vol def 4 keywords 1 volume_tau 1000 Time scale of volume evolution under constant pressure NPT_I or NPT_F in femtoseconds 2 volume_nhc_tau 100
29. tegration This number determines size of reciprocal space in the reference system Vpme parallel opt none hybrid full g Calculate the Ewald sum using the smooth particle mesh method in par allel using a parallel FFT 19 11 12 13 14 15 16 17 18 19 20 sep_Vander Waals on off If turned on then the VanderWaals component of the intermolecular in teraction energy is printed separately to screen inter_spline_pts 2000 Number of spline points used intermolecular interaction potential and derivative shift_inter_pe swit on off Keyword to determine how the real space intermolecular potential is switched off The swit option switches it off smoothly This option is recommended unless you are making direct comparisons with other codes The on option simply shifts it by a constant The off option is used is no switching or shifting is desired intra_block_min 50 When blocking intramolecular interactions this keyword determines min imum size of block pten_inter_respa 0 0 For NPT calculations using respa this keyword allows the user to estimate the size of the virial part of the pressure for use in the reference system Note this will not affect the total target pressure for the simulation pten_kin_respa 0 0 For NPT calculations using respa this keyword allows the user to estimate the size of the kinetic part of the pressure for use in the reference system No
30. ter controlling Vdw switching f r rm 48 bond parm 1 atoml1 Atom type 1 character data 2 Natom2 Atom type 2 character data 3 pot_type harmonic power series morse null Potential type of bond 4 fk Force constant of bond in K Angstrom 5 eq Equilibrium bond length in Angstrom 6 eq_res Respa Equilibrium bond length in Angstrom 7 alpha Morse parameter alpha in inverse Angstrom 6 r do exp a r ro 11 8 d0 Morse d0 in Kelvin r dolexp o r ro 1 49 pseudo parm 1 atom1 Atom type in character data 2 vps_typ local kb vdb null Pseudopotential type local Kleinman Bylander Vanderbilt or null 3 vps_file File containing the numerical generated pseudopotentials 4 Nn angl Number of angular momentum projection operators required 5 loc_opt Which angular momentum pseudopotential is taken to be the local 50 Coordinate Input Files At present the code will build topologies for the user However it will not build coordi nates Therefore the user must provide an initial input coordinate file see restart_type initial and in _restart_file sim_restart in The first line of the restart file must contain the num ber of atoms followed by a one followed by the number of path integral beads usually 1 The code will grow beads and only P 1 need be provided initia
31. ter than taking potentially inappropriate input parameters commands and forging ahead Also the code doesn t like to overwrite files because the designers have overwritten one too many useful files themselves and thought A very large file It might be very useful But now it is gone no the developers do not make it a habit to think in Haiku Finally many of the error messages are in colloquial American English a product of too many late nights writing code A language option has not yet been implemented The advisor may have to explain what Dude means However the code does have a lot of error checking because there is nothing worse than Wind catches lily Scatt ring petals to the wind Segmentation fault which leads one to believe Errors have occurred I cannot tell where or why Lazy programmers This manual was also a late night accomplishment Generally the particular setting or variable with which the code is unhappy is specified in the error message Finally note that not all keywords are described in detail if at all in this manual The reason for this is that the user does not need to know about all of the advanced level keywords in order to run the code Many of these keywords are only of interest to developers or experts interested in doing rather abstruse things Thus if it says below that n keywords are possible within given meta keyword but fewer than n are actually explained don t worry If yo
32. to vary but not the angles monoclinic allow only angle to vary from 90 degrees or none all lengths and angles vary min_atm_com_fix no yes During atomic minimization calculation keep the center of mass of the system fixed 12 sim_ nhc_def 14 keywords 10 atm_nhc_tau_def 1000 Time scale in femtoseconds on which the thermostats should evolve Gen erally set to some characteristic time scale in the system atm_nhc_len 2 Number of elements in the thermostat chain Generally 2 4 is adequate Vespa steps nhc 2 Number of individual Suzuki Yoshida factorizations to be employed in in tegration of the thermostat variables Only increase if energy conservation not satisfactory with default value yosh_steps_nhc 1 3 5 7 Order of the Suzuki Yoshida integration scheme for the thermostat vari ables Only increase if energy conservation not satisfactory with default value init_resmp_atm_nhc on off If turned on atomic thermostat velocities will be initially resampled from a Maxwell distribution resmpl_atm_nhc 0 Resample coefficient thermostat velocities with a frequency equal to the number in curly brackets 0 indicates no resampling respa_xi_opt 1 2 3 4 Depth of penetration of thermostat integration into multiple time step levels Larger numbers indicate deeper penetration 1 indicates thermostat variables are updated at the beginning and end of every step XO option
33. u really want to know contact the developers Simulation Keyword Dictionary The following commands maybe specified in the simulation setup file sim gen def 21 keywords sim run def 30 keywords sim nhc def 15 keywords sim write def 29 keywords sim list def 14 keywords sim class PE def 25 keywords sim vol def 4 keywords sim cp def 36 keywords Bo EL sue LT aee Aper xS sim pimd def 11 keywords mL m sim velo corel 14 keywords m m sim msqad corel 5 keywords m N sim_iikt_iso_corel 10 keywords m c2 sim ickt iso corel 7 keywords 14 sim rdf corel 9 keywords A complete list of all commands employed including default values are placed in the file sim write def sim name def sim input out sim gen def 24 key words 1 restart_type initial restart pos restart posvel restart all Option controlling how the coordinate input file is read in initial Start using initial format with atomic positions in angstroms restart pos Restart only the atomic positions Velocities and ther mostat velocites if used are sampled from a Maxwell distribution restart posvel Restart both atmoic position and atomic velocities Thermostat velocities if used are sampled from a Maxwell distribu tion restart all Restart atomic positions velocities and thermostat ve locities if used 2 Nsimulation
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