Re: water molecules "collapse" during equilibration

From: Nicholas M Glykos (
Date: Fri May 29 2009 - 12:49:56 CDT

> 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?

Get a new (unmodified) copy of top_all27_prot_lipid.inp and use that.

          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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