[gmx-users] Polymer Simulations

[NIKHIL JOSHI]

Dear Sir


1) First i made my molecules whole by using command:

trjconv_mpi -s run.tpr -f run.xtc -pbc whole -o runwhole.xtc

2) Then i used nojump command:
trjconv_mpi -f runwhole.xtc -pbc nojump -o runwholenojump.xtc
3) then i did the centre the system:
4) Finally i put the whle system in the box

after following these steps, still the same error.


On Thu, Mar 9, 2017 at 10:33 AM, NIKHIL JOSHI <nikhil.joshi926 at gmail.com>
wrote:

> Thank you for the reply sir.
>
> On Wed, Mar 8, 2017 at 6:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/8/17 6:13 AM, NIKHIL JOSHI wrote:
>>
>>> hii
>>>
>>> I am simulating polymer of 100 chains of 12 monomer repeat units. After
>>> the
>>> final run, if I observe the final structure in vmd, the structure is
>>> splitting into two. What will be the reason and how to rectify it. Please
>>>
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Bo
>> undary_Conditions
>>
>> find the attachment.
>>>
>>>
>> The mailing list does not accept attachments.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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>
>