From: EPF \(Esben Peter Friis\) (EPF_at_novozymes.com)
Date: Mon Mar 06 2006 - 03:48:06 CST
Hi again
Even though they use the same force field, the simulation engines of
NAMD and Charmm are not entirely identical (?). Even if you could read
the velocities from the charmm run into NAMD, I believe it would still
lead to a different result than continuing in Charmm. It is probably ok
to do the equilibration in Charmm, and then reassign the velocities and
do the production in NAMD. But, as Michel points out, it would probably
be better to start from scratch, if it is not an enourmous amount of CPU
time.
Best wishes
Esben
> -----Original Message-----
> From: Himanshu Khandelia [mailto:hkhandel_at_dtc.umn.edu]
> Sent: 5. marts 2006 21:51
> To: EPF (Esben Peter Friis)
> Cc: namd-l_at_ks.uiuc.edu
> Subject: RE: namd-l: starting simulation in charmm,
> continuing in NAMD ?
>
>
> Hi,
>
> I can write out a psf and a pdb in charmm and convert to NAMD
> formats, sure. But the psf does not contain the velocities,
> so the velocities will need to be re-initialized in NAMD,
> which will, thus, lead to an entirely new simulation. Am I wrong ?
>
> ===================================================
> Himanshu Khandelia
>
> Doctoral Candidate,
> Kaznessis Research,
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
>
> Mailing Address:
>
> 499, Walter Library,
> 117, Pleasant St. SE,
> Minneapolis, MN 55455
>
> Phone(o): 612-624-4945
> ===================================================
>
>
> On Sun, 5 Mar 2006, EPF (Esben Peter Friis) wrote:
>
> >
> >
> > Hi Himanshu
> >
> > I don't know if you can use the Charmm restart files in
> NAMD, but most
> > likely not. Is it possible for you to use charmm for writing out a
> > crd/psf file pair for the final state of your charmm simulation? If
> > so, you can continue by converting the charmm crd/psf pair
> to a NAMD
> > pdb/psf pair using the two scripts at
> >
> > http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAndCHARMM
> >
> >
> > Best wishes
> >
> > Esben
> >
> >
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu on behalf of Himanshu Khandelia
> > Sent: Sun 2006-03-05 18:23
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: starting simulation in charmm, continuing in NAMD ?
> >
> > Hi,
> >
> > I was wondering if it was possible to have started a simulation in
> > charmm, and continue it in NAMD ? I have already crossed
> equilibration
> > and am into production while using charmm. Given that the
> force fields
> > are the same, will this cause problems ? Importantly, will
> I be able
> > to use the charmm restart file in NAMD ? If not, I will
> obviously have
> > to restart the simulation run from scratch. Thank you very much for
> > your inputs,
> >
> > -Himanshu
> >
> >
>
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