RE: regenerating PSF file

From: Pijush Ghosh (
Date: Wed May 18 2005 - 10:01:51 CDT

Hello Cetin
    Yes actually you are right, in InsightII you can generate .psf file
after MD and this may be different from that of your initial one depending
upon atom positions and bond distance criteria, but in NAMD its different,
as Michael mentioned if you are not breaking the bonds by hand you can use
the same psf file again and again. PSF file in NAMD contains no information
about the non covalent bonds; you have to actually decide from coordinate
positions depending upon your own definition of non covalent bonds. Hope
this helps.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA
-----Original Message-----
From: [] On Behalf
Of Cetin Baloglu
Sent: Wednesday, May 18, 2005 2:51 AM
Subject: Re: namd-l: regenerating PSF file

Thanks for the answer Michael,
Actually I am curious about non-covalent bonds. Do psf files contain
information about these bonds and the related atoms? Also angles,
dihedral angles changes but with the same psf file we use the same
values. I saw discover in insightII producing the protein structure
file after md is done and this made me think about regenerating the
psf file.

On 5/18/05, Michael Grabe <> wrote:
> Cetin,
> do you break these bonds by hand? if so, then you certainly
> need to generate new psf files, but no bonds will be breaking
> during your high temperature runs.
> -michael
> On May 17, 2005, at 11:07 PM, Cetin Baloglu wrote:
> > Hi,
> >
> > I am doing simulations to observe temperature effects on proteins. I
> > use same psf file for every experiment, which inputs are outputs of
> > previous experiments. However, I am thinking if this is a mistake or
> > not as psf file contains bond information that is to be broken in high
> > temperatures.
> >
> > Cetin Baloglu
> >
> >
> >
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> Post-doctoral Fellow
> Howard Hughes Medical Institute
> University of California, San Francisco
> 1550 4th Street GD482
> San Francisco, CA 94143
> tel: ++ 415.476.4021

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:46 CST