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

[John Shultz]

Justin,

I finally got a chance to get back to this. I read the make_ndx
instructions. Unless I am mistaken, I guess that is what you use to
merge groups.

Thanks,

Jack

On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
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