[gmx-users] tpbconv subset

[Justin A. Lemkul]

John Shultz wrote:
> I modified the .mdp file, created a full system tpr, then ran it
> through tpbconv, then ran mdrun using the original xtc. It says the
> atom numbers don't match.
> 
> 
> mdrun -rerun md.xtc -v -s lig.tpr
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.5
> Source code file: md.c, line: 859
> 
> Fatal error:
> Number of atoms in trajectory (37655) does not match the run input file (65)
> 
> -------------------------------------------------------
> 

This time it appears that you have saved your whole system rather than the some 
other subset (ligand only?).  Check your xtc-grps to see what was written.

-Justin

> On Sun, May 23, 2010 at 5:16 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> John Shultz wrote:
>>> Justin,
>>>
>>> Only problem is I need to change this parameter
>>> energygrps
>>>
>>> to track the energy on specific groups in the simulation. Is there a
>>> way to modify the simulation parameters to track these energies?
>>>
>> Modify the .mdp file the way you need to, create a full-system .tpr file,
>> then run it through tpbconv.
>>
>> -Justin
>>
>>> On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> John Shultz wrote:
>>>>> I want to run a subset of an original trajectory. I know how to get
>>>>> the tpr consisting of the subset. How do I modify the simulation with
>>>>> a new mdp file and then run the mdrun? I was referencing these
>>>>> instructions
>>>>>
>>>> If you have a .tpr file, then the .mdp file is a step backwards.  You
>>>> don't
>>>> need it.
>>>>
>>>> Assuming you want to do some sort of re-run procedure, you simply have to
>>>> run:
>>>>
>>>> mdrun -s subset.tpr -rerun original.xtc
>>>>
>>>> (where original.xtc is your trajectory file that contains the same subset
>>>> of
>>>> atoms as subset.tpr)
>>>>
>>>> -Justin
>>>>
>>>>> http://manual.gromacs.org/current/online/tpbconv.html
>>>>> 3nd. by creating a tpx file for a subset of your original tpx file,
>>>>> which is useful when you want to remove the solvent from your tpx
>>>>> file, or when you want to make e.g. a pure Ca tpx file. WARNING: this
>>>>> tpx file is not fully functional.
>>>> --
>>>> ========================================
>>>>
>>>> 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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> 

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

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

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