water molecules "collapse" during equilibration

From: enz1+_at_pitt.edu
Date: Fri May 29 2009 - 11:38:06 CDT


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

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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