[gmx-users] visualize gromacs trajectory in VMD

[Justin Lemkul]

On 4/1/14, 11:39 AM, sunyeping wrote:
> Dear all,
> I am trying to visualize gromacs trajectory in VMD. when I load my .gro file, the GUI window of VMD show a structure that seems to be correct. However, when I load .xtc or .trr file, the strucute shown is seriously deformed. Most bonds become very long and the structures looks very strange. Could anyone tell me how to show the trajectory correctly? Thanks.

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

-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 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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