[gmx-users] Polymer Simulations

[NIKHIL JOSHI]

Thank you sir for your reply.

On Tue, Mar 14, 2017 at 6:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/14/17 8:36 AM, NIKHIL JOSHI wrote:
>
>> 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.
>>
>>
> It should be much simpler:
>
> trjconv -s run.tpr -f run.xtc -pbc mol -center
>
>
> -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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