[gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

Justin Lemkul jalemkul at vt.edu
Thu Feb 4 19:23:00 CET 2016

On 2/4/16 1:18 PM, sun wrote:
> Hello Everyone
> I have performed a md simulation if protein in water for 10ns and frames were obtained after every 10ps. I wanted to visualize the.gro and trajectory file in VMD, without water, so I prepared an index file containing protein only. Using editcon i removed water from md.gro as well but I loaded the files in VMD, 1000 time frames are loaded but I cannot see any change in structure or per frame conformation. The protein is still. I am not clear what to do. I tried keeping water in .trr and then in .gro and repeated steps but no results. When I use original .trr and .gro, only then i visualize the change in structure. Please help me

You can't load coordinate and trajectory files with different numbers of atoms. 
  If you strip the waters from the starting .gro file, you must also do this for 
the trajectory (that's what eats up all the memory in VMD, anyway).



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


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