Restarting A NAMD job with velocity file

From: neville forlemu (
Date: Mon Mar 22 2010 - 15:50:07 CDT


--- On Wed, 2/24/10, Axel Kohlmeyer <> wrote:

From: Axel Kohlmeyer <>
Subject: Re: namd-l: psfgen error
To: "Syed Kashif Zafar" <>
Date: Wednesday, February 24, 2010, 12:19 AM

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--0-1514318284-1269291007=:53372--

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