[gmx-users] Polymer Simulations

[Justin Lemkul]

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

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