From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun Mar 05 2006 - 15:19:44 CST
Well, if you don't have your velocities, then you can set an initial
temperature (i.e., 300K) and it will, in theory, be enough to restart
your simulation... But yes, the best will be to start your simulation
from scratch...
2006/3/5, Himanshu Khandelia <hkhandel_at_dtc.umn.edu>:
> 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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