Re: Vibrational mode analysis

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Jun 15 2006 - 21:01:04 CDT

> You can also check out GROMACS and why not AMBER, as Michael suggested.

Thanks. The thing is that I would like to run it with the CHARMM force
field, because I have performed MD with the CHARMM force field and I want
to compare normal mode analysis with essential dynamics. It could also be
that the force field does not matter much for NMA.

Gianluca

> 2006/6/15, Gianluca Interlandi <gianluca_at_u.washington.edu>:
> > Hello Michel,
> >
> > Do you know of any tutorials how to do it with CHARMM? I know the vibran
> > module of CHARMM ca do it.
> >
> > Thanks,
> >
> > Gianluca
> >
> > On Thu, 15 Jun 2006, L. Michel Espinoza-Fonseca wrote:
> >
> > > Gianluca,
> > >
> > > Regarding the first question, no, currently it is not possible to
> > > perform normal mode analysis with NAMD.
> > >
> > > In respect to the second question, you could use the CHARMM program in
> > > order to perform such analysis. I also think that you can do it with
> > > the aid of the GROMACS package -which is freely available-.
> > >
> > > Michel
> > >
> > > 2006/6/15, Gianluca Interlandi <gianluca_at_u.washington.edu>:
> > > > Is it possible to perform vibrational mode analysis with NAMD?
> > > >
> > > > If not, does anybody know of a program wich does vibrational mode
> > > > analysis
> > > > using the CHARMM force field?
> > > >
> > > > Thanks a lot,
> > > >
> > > > Gianluca
> > > >
> > > > -----------------------------------------------------
> > > > Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> > > > +1 (206) 685 4432
> > > > +1 (206) 714 4303
> > > > http://biocroma.unizh.ch/gianluca/
> > > >
> > > > Postdoc at the Department of Bioengineering
> > > > at the University of Washington, Seattle WA U.S.A.
> > > > -----------------------------------------------------
> > > >
> > >
> >
> > -----------------------------------------------------
> > Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> > +1 (206) 685 4432
> > +1 (206) 714 4303
> > http://biocroma.unizh.ch/gianluca/
> >
> > Postdoc at the Department of Bioengineering
> > at the University of Washington, Seattle WA U.S.A.
> > -----------------------------------------------------
> >
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4432
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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