[gmx-users] How to remove water

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Sep 3 01:36:01 CEST 2003

>I read in documentation that we have to use trjconv command for it, but 
>what options do i use for doing this?  Do i need to make a seperate index 
>life for this??
>what command should i give to carry out this task?

Generate an index file using make_ndx.  Have in there a group that contains 
all the molecules you want to remain in the trajectory, so that may be 
protein and ions.  Then run trjconv using that index file and select the 
index group with the protein and ions in it.

make_ndx -f conf.gro -o index.ndx
trajconv -f traj.xtc -o traj_nw.xtc -n index.ndx

Catch ya,

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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