[gmx-users] Отв: Make DNA stay in the center of the box during Simulation

[Justin Lemkul]

On 12/6/14 10:03 AM, Hovakim Grabski wrote:
> But if I use gmx trjconv -s md_1_1.tpr -f md_1_1.xtc -o md_1_1CentNew_noPBC.xtc
> -pbc mol -ur compact -center, select DNA as the center group,  DNA molecule
> jumps back and forth, is there any way I can solve it?
> I use Gromacs 5.0.1
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

In most cases, you need several rounds of trjconv, in the proper order, to get 
your system in a proper state for visualization.  With a molecule like dsDNA, it 
can be "centered" when both strands are at opposite "ends" of the box, because 
the geometric center of the strands coincides with the geometric center of the 
box.  So extra steps need to be taken, sometimes with custom index groups.

-Justin

-- 
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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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