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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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