Re: psfgen error

From: Axel Kohlmeyer (
Date: Wed Feb 24 2010 - 00:19:44 CST

On Tue, Feb 23, 2010 at 11:44 PM, Syed Kashif Zafar
<> wrote:
> Hi all,
>    I have an equilibrated pdb patch for a DMPC bilayer. Now I want to add
> water and run it using NAMD.But in the pdb patch the molecules are wrapped
> and when I use psfgen and topology file to generate the psf, it connects
> the atoms across the periodic cell giving bonds that exist across the
> periodic cell. Can anyone suggest how I can unwrap the coordinates in the
> pdb that I have or some other solution.

actually, there is no real problem if you use the same simulation cell size.
these atoms will be wrapped back during the force evaluation anyway.s.

you can use, "pbc join" in VMD to wrap those atoms back, provided your
.pdb file does have the cell size information.


> Thanks
> waiting for helpful response
> kashif
> junior research fellow
> H.E.J Research Institute
> Karachi, Pakistan

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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