[gmx-users] How to use deuterium order parameters

Igor Marques igor.dragon88 at gmail.com
Wed Nov 2 15:26:16 CET 2011

On Wed, Nov 2, 2011 at 2:06 PM, Alex <alexbioinfo at yahoo.com> wrote:

> Dear All
> I'd like to perfom a deuterium oerder parameters analysys in a system with
> + 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
yes, that's a way to do it.

> I need as well to make two index files: for sn1 and sn2 chains of DPPC.
yes, that is correct.

> Have I to run g_order in both ndx files (sn1 and sn2)?
yes, that is also correct. make sure to write two different output files
(sn1.out and sn2.out)

> Thanks
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