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