[gmx-users] pbc problem

[Justin Lemkul]

On 5/14/14, 7:54 AM, elham tazikeh wrote:
> dear gromacs users
> i did simulate zinc and copper ion on human growth hormone protein
> when i saw my md.gro and md.xtc files by VMD software
> i found out my system isn,t in the box(cubic)
> i tried to solve this problem by :
>
> trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol
>
> but there is this problem,again.
> could you please help me
>

Often times, a single pass of trjconv is insufficient.  At the very least, try 
using the (intuitive) -center option.  Otherwise, consult 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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