[gmx-users] NVT and NVE

[JMandumpal]

Dear Mark,

Thank you very much for the reply.
Well I used the following job script:
#!/bin/bash
#PBS  -l vmem=800MB
#PBS  -l ncpus=4
#PBS  -l jobfs=10MB
#PBS  -l software=gromacs
#PBS  -l other=mpi
#PBS  -q express
#PBS  -wd
module  load gromacs/3.3.2                                                                                                                                                              
grompp_d -np $PBS_NCPUS -f mdout_NVE.mdp -p topol.top -c conf_100ps.gro -t pr.trr  -o binary.tpr
mpirun mdrun_mpi_d -s binary.tpr -o pr1.trr -c output_1.gro -g topol.log
Note: pr.trr is the trajectory from 100ps NVT simulations, and conf_100ps.gro is the equilibrated box from the same.
--------------------------------------------------------------
MY .mdp file, for running NVE simulation after a 100ps equilibration with NVT, is pasted here:
title                    = Howdie
cpp                      = /usr/bin/cpp
; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.0015;
nsteps                   = 40000
; For exact run continuation or redoing part of a run
init_step                = 100001
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = SOL
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint            = 1000
; Output frequency for energies to log file and energy file
nstlog                   = 10000
nstenergy                = 1000
; Output frequency and precision for xtc file
nstxtcout                = 0
xtc-precision            = 1000
; select multiple groups. By default all atoms will be written.
; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions:
pbc                      = xyz
; nblist cut-off
rlist                    = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = pme
rcoulomb                 = 1.0
ewald_rtol               = 1e-5  ; since erfc(sigma*rcutoff)=ewald_rtol
optimize_fft             = yes
; Relative dielectric constant for the medium
epsilon_r                = 1  ; for water
; Method for doing Van der Waals
vdw-type                 = cut-off
rvdw                     = 1.0
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12 ;
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_geometry           = 3d
epsilon_surface          = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = no
; Groups to couple separately
tc-grps                  = SOL
; Time constant (ps) and reference temperature (K)
tau-t                    = 0.1
ref-t                    = 300
; Pressure coupling
Pcoupl                   = no
Pcoupltype               = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 0.5
compressibility          = 4.5e-5
ref-p                    = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
gen-temp                 = 300
gen-seed                 = 173529
; OPTIONS FOR BONDS
constraints              = all-bonds
constraint_algorithm     = shake
shake_tol                = 0.0001
morse                    = no
--------------------------------------------------------
I suspect I made something wrong in these variables; Could anyone please correct it?
tinit                    = 0
; For exact run continuation or redoing part of a run
init_step                = 100001

regards,
Jestin




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