[gmx-users] rerun trajectory does not match input file

John Shultz jackygrahamez at gmail.com
Thu May 13 14:56:58 CEST 2010


I am trying to rerun a simulation using this command
mdrun -rerun -v -deffnm md

I think I must have made a mistake when I prepared the original mdp
file because I get this message
Number of atoms in trajectory (3883) does not match the run input file (37770)

I have these files in my directory
Complex.top  ener.edr  job.xml  md.cpt  md.edr  md.gro  md.log  md.mdp
 md_prev.cpt  md.tpr  md.trr  md.xtc  traj.trr

Here is my mdp file, should I remove entries for xtc_grps and
energygrps to avoid this issue?

integrator = md
nsteps = 50000
dt = 0.002
nstvout = 5000
nstlog = 500
nstenergy = 250
nstxtcout = 5000
nstxout = 5000
xtc_grps = Protein LIG
energygrps = Protein  SOL
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist = 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
Pcoupl = parrinello-rahman
PcOupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
gen_seed = 805087



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