[gmx-users] RDF of hydroxyl groups
msiwko at ibmb.uni.wroc.pl
Mon Jun 21 16:39:39 CEST 2004
I'm working on simulation of mixed bilayer (DMPC and some kind of phenolic
lipid). My lipid in head has aromatic ring with two hydroxyl groups.
I want to know the change in hydratation of this mixed bilayer via function of
concentration of inserted lipids and tails lenght.
I calculated rdf in two ways.
1. For 2 hydrogens of phenolic lipid hydroxyl groups (as a one group in index
file - H5_H13) - reference group and OW (oxygen in water), OA-P-OB-OC-OD
(phosphate group of DMPC) and also for two carbonyl groups OE-C1A-Of and
2. Reference group OW (solvent) and hydrogens from hydroxyl groups and phosphate
and carbonyl groups as above. This set-up looks reasonable.
I wonder why in first set-up rdf for one carbonyl group OE-C1A-OF is so
large - 44 where usually in papers this values are around 2-4?
Is the correct way I define groups in index file?
Pls, some hints.
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