From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Sep 19 2007 - 10:39:23 CDT
Yes, it is possible to analyze charmm trajectories using NAMD. You will
need to change the psf and the pdb files that you have in CHARMM to a VMD
suitable format (sometimes even this is not necassary). This can be done
by using scripts available on the NAMD website.
I have used both CHARMM and VMD for analysis, and I personally think that
CHARMM can be used to most of the analysis possible with VMD (and more).
Good luck !
----------------------------
Himanshu Khandelia, PhD
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
University of Southern Denmark (SDU)
Campusvej 55,
Odense M 5230, Denmark
Phone: +45 6550 3510
Fax: +45 6550 4048
email: hkhandel_at_memphys.sdu.dk
WWW: www.memphys.sdu.dk/~hkhandel
-----------------------------
On Wed, 19 Sep 2007, Philip Peartree wrote:
> As far as I know it should be the DCD files are in the same format. The psf
> might need changing (if you need it). For that all you need to do it make
> charmm export it in XPLOR format. Follow normal writing procedures (i.e. open
> a
> unit etc) and use the command: write psf card xplor followed by the unit name.
> Should be ok then.
>
> Philip Peartree
>
>
> Quoting priyanka srivastava <priyankaps4_at_yahoo.com>:
>
> > Dear Namd users,
> >
> > This is my first post in this forum and I am very new
> > to NAMD.
> > I have seen some studies wherein NAMD has been used to
> > calculate the pressure profiles of bilayer systems.
> > I carried out bilayer simulation using Charmm and wish
> > to use the analysis tools (specifically that of
> > pressure profile calculation) from NAMD using the
> > trajectories generated from Charmm.
> >
> > Is it possible to use charmm generated trajectory
> > files in NAMD for analysis purposes?
> >
> > Regards,
> > Pri...
> >
> >
> >
> >
> > ____________________________________________________________________________________
> > Tonight's top picks. What will you watch tonight? Preview the hottest shows
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> >
>
>
>
>
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