[gmx-users] Trajectory optimization - 2 chains are separated

[Justin Lemkul]

On 2/15/20 9:52 AM, Marwa Abd El Kader wrote:
> Dear Justin,
> I 've tried centering on one chain and the same problem still exists, any
> suggestions?

If centering on one chain via trjconv -center -pbc mol does not yield 
dimers, then I suspect the two chains are not actually associated and 
what you're observing is not actually a PBC issue, unless your box is 
too small and PBC jumps are unavoidable even if one species is properly 
centered.

-Justin

> On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote:
>>> Dear Justin,
>>> Would you please tell me how, give me an example code, because I'm a
>> novice?
>>
>> The same thing you did before but instead of trying to select
>> interfacial residues, make an index group of one of the protein chains
>> and select it for the centering group.
>>
>> -Justin
>>
>>> Thanks in advance,
>>> Marwa
>>>
>>> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
>>>>> Dear gmx-users mailing list team,
>>>>> I want to know how to fix the separation of 2 chains after the
>> production
>>>>> run. I'm trying different combinations of trjconv after creating an
>> index
>>>>> file having a specific residue(s) on the interface between the 2
>> chains,
>>>>> but nothing is working. I fixed this issue before but when there was
>> only
>>>>> one chain, now with 2 chains, I don't know how to rejoin them together
>>>>> again. Can you suggest me any solution, please?!
>>>>> *N.B: the 2 chains are considered as one when selected in VMD
>>>> Center on a single chain rather than trying to work with the interface
>>>> residues.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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