From: neville forlemu (neville_forlemu_at_yahoo.com)
Date: Mon Mar 22 2010 - 15:50:07 CDT
Hello
--- On Wed, 2/24/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Subject: Re: namd-l: psfgen error
To: "Syed Kashif Zafar" <skashifzafar_at_yahoo.com>
Cc: namd-l_at_ks.uiuc.edu
Date: Wednesday, February 24, 2010, 12:19 AM
On Tue, Feb 23, 2010 at 11:44 PM, Syed Kashif Zafar
<skashifzafar_at_yahoo.com> 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--
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:36 CST