[gmx-users] regarding pbc issue

[Justin Lemkul]

On 1/17/18 11:23 AM, Rose wrote:
> I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes?
> just will show them broken (as they really are) yes?

In the context of the question I was answering, "broken" means that it 
appears bonds have broken and molecules appear at either side of a 
periodic boundary. That instance is always fixed by proper use of 
trjconv. Bonds can't break or form during classical MD, so if trjconv 
leaves "broken" molecules behind, then you've got a topology issue. But 
I'd wager that about 99.999% of the cases that involve "broken" 
molecules are normal PBC issues and nothing more.

But, to answer your question, no, trjconv won't fix a situation in which 
the user has supplied an incorrect topology.

-Justin

> Sent from my iPhone
>
>> On Jan 17, 2018, at 18:15, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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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

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