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

mary ko maryko2019 at yahoo.com
Tue Mar 12 03:52:12 CET 2019

 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 ? 
    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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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