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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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