[gmx-users] regarding pbc issue

[Vidya R]

Hi Justin,

I got the same result as you said.

What confused me was,  when I viewed movie.pdb file generated by the
following command,

 gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 10000.0 -n
index.ndx -o movie.pdb


two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be).  They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Thanks,
Vidya.R



On Sat, Jan 13, 2018 at 7:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/13/18 7:53 AM, Vidya R wrote:
>
>> Hi gmx users,
>>
>> I used the following commands after simulation run (organic compound in
>> water, to calculate rdf)
>>
>>
>>
>>   gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
>> gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
>>   gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o
>> newtraj.xtc
>>
>>
>> To use the following command, which xtc file should I use?
>>
>> gmx rdf -f ---.xtc -n index.ndx
>>
>> *prd or newtraj.xtc?*
>>
>> Please clear my doubt.
>>
>
> Run both and see if there is a difference. gmx rdf should be PBC-aware, so
> you should get the same result.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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