[gmx-users] tpbconv subset

[John Shultz]

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)

-------------------------------------------------------

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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