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

[Justin A. Lemkul]

John Shultz wrote:
> 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.
> 

Yep, that's the purpose of make_ndx.

-Justin

> 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
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface
>>>> or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 

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

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

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