[gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/17/18 9:40 AM, Rose wrote:
> You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes?

mdrun writes "broken" coordinates because the physics does not depend on 
our visualization convenience. Most programs account for PBC. Some 
don't. It is generally a safe practice to just make molecules whole as 
your first step in trjconv and avoid any ambiguity.

-Justin

> 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
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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