[gmx-users] How to remove the water from my .trr file?

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Aug 10 00:53:32 CEST 2004

>I am trying to remove the water from my .trr file. I think I need to use
>tpbconv, but I don't know how to use tpbconv....
>Would you tell me how to use tpbconv to remove water from my .trr file?

First make an index file using make_ndx and ensure that you create a group 
the contains all the molecules/atoms you want in the final trajectory file 
minus the water.

Then run trjconv with the -f, -o and -n switches, and select the 
appropriate index group when prompted.

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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