John Shultz wrote:
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?
You can, but it won't fix anything. Your original .xtc file saved only the
coordinates of the Protein and LIG (per your output options), but your .tpr file
has all of these atoms, regardless of what you choose to save. You can,
however, create a .tpr file that has a just these atoms by passing your original
.tpr file to tpbconv, using a suitable index group.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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