[gmx-users] SPC - hydrogen bonding..
gk237 at cam.ac.uk
Tue Aug 5 17:08:01 CEST 2003
I am simulating a pentapeptide as a switterion in explicit SPC water. I
want to investigate the role of water during some folding events
(beta-turns) , especially when it comes down to water--> peptide
hydrogen bonding. We have implemented an algorithm for that, with
geometrical criteria, similar to GROMACS one.
The question is , i really see a "trend" of the water molecules to be
hbonded to the peptide-NH's (water oxygens) but there is no significant
OH2---O=C-peptide (except of the terminal COO-)...
I was really wondering if this could really be a normal situation , or
maybe an artifact due to SPC parameters...
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