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

[Justin A. Lemkul]

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

You need to make a custom group that merges these two.

-Justin

> 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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> 

-- 
========================================

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

========================================