From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 14:14:19 CDT
Removing the extra H-H bond won't cause the behavior you are seeing,
I believe. It sounds like instead you have no angle term for water
in your psf. How did you generate it?
On May 29, 2009, at 11:38 AM, enz1+@pitt.edu wrote:
> Hi,
>
> My pdb/psf file for MD is a protein embedded in a bilipid layer
> with water
> molecules above and beneath. Whenever I run equilibration the water
> molecules "collapse", e.g, the two H atoms just keep getting closer to
> each other during the first steps of the MD till they are on top of
> each
> other.
>
> I had previously changed the topology file generator
> (top_all27_protein_lipid.inp) and removed the extra H-H bond there
> to get
> water molecules with just the two bonds between OH2-H1 and OH2-H2).
>
> What can I do to solve this?
>
> Thanks in advance
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:52 CST