[gmx-users] regarding pbc issue

[Rose]

You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes?

Sent from my iPhone

> On Jan 17, 2018, at 16:19, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> On 1/17/18 5:51 AM, Vidya R wrote:
>> 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.
> 
> Making molecules whole should always be the first step. If you try to remove jumps with "broken" molecules, what you visualize will be garbage. A separate issue is with respect to the analysis programs - many are PBC-aware and can handle the original trajectory without manipulation.
> 
> -Justin
> 
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> Justin A. Lemkul, Ph.D.
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> Virginia Tech Department of Biochemistry
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