[gmx-users] regarding pbc issue

Thu Jan 18 13:44:36 CET 2018

On 1/17/18 12:06 PM, Rose wrote:
> Thank you so much,I've got it now.
>
> we know that for example 2 molecule can not stick to each other they just close enough till repulse  each other.
> Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so what would be my criterion and clue to say that:"that's enough, you shouldn't pull it MORE?"
>
> Totally, how can i know the Max pulling ?
>
> I have PMF schemes which show repulsion( after interaction distance the potential get less minus and tend to get more positive but they just stop in 0kJ and not any positive potential. It happened for every AA which i pull it through sheet, so i doubt to my results.

A PMF of zero means the biased groups are (effectively) no longer 
interacting. You should expect this.

This thread is well off topic of the original post; if you have further 
questions, start a new thread to avoid hijacking this one and 
complicating the archive further.

-Justin

> Sorry for poor english
>
> With regards
> Sent from my iPhone
>
>> On Jan 17, 2018, at 19:57, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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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

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