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

[Justin A. Lemkul]

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

-- 
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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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