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

[John Shultz]

Thank you Justin, is there a way I can choose both Protein LIG? It has
the following options for me

Reading toplogy and shit from md.tpr
Reading file md.tpr, VERSION 4.0.5 (single precision)
50000 steps (100 ps) remaining from first run.
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 37770 elements
Group     1 (     Protein) has  3848 elements
Group     2 (   Protein-H) has  1980 elements
Group     3 (     C-alpha) has   244 elements
Group     4 (    Backbone) has   732 elements
Group     5 (   MainChain) has   974 elements
Group     6 (MainChain+Cb) has  1206 elements
Group     7 ( MainChain+H) has  1198 elements
Group     8 (   SideChain) has  2650 elements
Group     9 ( SideChain-H) has  1006 elements
Group    10 ( Prot-Masses) has  3848 elements
Group    11 ( Non-Protein) has 33922 elements
Group    12 (         LIG) has    35 elements
Group    13 (         SOL) has 33807 elements
Group    14 (          Na) has    46 elements
Group    15 (          Cl) has    34 elements
Group    16 (       Other) has 33922 elements
Select a group:


On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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