[gmx-users] Removing molecules from .trr and .gro

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Sep 12 02:42:14 CEST 2002

I have gone through the manual, FAQ and searched this emailing list and 
haven't been able to find anything on this.  If I have missed it, sorry.

I am looking to remove water from my mdrun output files, .trr and .gro, to 
make them significantly smaller and faster to handle.

Using trjconv I have managed to remove the water from the .trr file no 
problem at all, reducing the file size significantly.

Problem is that you need a corresponding .gro file to be able to visualise 
the system in VMD.  The .gro file has all the water molecules still in it, 
so the two are incompatable.

Does one of the scripts provided enable this to be performed?

Thank you for any assistance or direction.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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