[gmx-users] tpbconv subset

[Justin A. Lemkul]

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

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