[gmx-users] How to use deuterium order parameters

Alex alexbioinfo at yahoo.com
Wed Nov 2 15:06:18 CET 2011

Dear All

I'd like to perfom a deuterium oerder parameters analysys in a system with DPPC 
+ Protein + Water
I read that I've to make an index file that contains one group each for every 
carbon atom in the acyl-chain (starting
with the carbonyl-carbon and going further down).
Where can I get carbon atoms index in the acyl-chain to group them? Have I to 
open the DPPC in pdbviewer

I need as well to make two index files: for sn1 and sn2 chains of DPPC.
Have I to run g_order in both ndx files (sn1 and sn2)?


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