[gmx-users] VMD movie making-remove water molecules from .trr after a simulation

Justin Lemkul jalemkul at vt.edu
Tue Mar 12 17:34:08 CET 2019

On 3/11/19 10:42 PM, mary ko wrote:
>   Thank you Justin. Is it possible to choose protein and ligand separately (e.g. 1|13) in the trjconv, since I chose protein-ligand subgroup which was taken as a whole and ligand can not be distinguished individually ? Or should I do any modifications in VMD ?

I don't understand the assertion that the ligand "cannot be 
distinguished individually." You can save whatever coordinates you want 
using trjconv. How you visualize them is a separate issue, and perhaps 
one better suited for the VMD users mailing list.


>      On Monday, March 11, 2019, 6:32:22 PM EDT, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/11/19 6:01 PM, mary ko wrote:
>> Dear all
>> How can I make a movie from a protein-ligand simulation in VMD? I opened complex.pdb and md-fit.trr and  the movie is shown but due to the large number of water molecules it freezes after some frames. How can I remove solvent molecules from the md-fit.trr? Any other suggestions how to make the movie without freezing?
> Use trjconv to save whatever subset of coordinates you want.
> -Justin


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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