[gmx-users] g_order question

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 31 20:37:22 CEST 2010

On 2010-08-31 20.26, Paymon Pirzadeh wrote:
> Hello,
> It is said in the mannual that g_order compute the order parameter per
> atom for carbon tails. Can it also calculate order (degree of
> tetrahedrality) for water molecules if only water oxygens are selected
> in index file? The reference paper is for water molecules though. Also,
> does it calculate an average value or give a profile as a function of
> time?
> thanks,
> Paymon
Have you tried it?

You can compute tetrahedrality for water, and also do it in slices 
accross the box axis. It computes the average over time.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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