Re: water molecules "collapse" during equilibration

From: JC Gumbart (
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, 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

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