RE: starting simulation in charmm, continuing in NAMD ?

From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Sun Mar 05 2006 - 14:50:39 CST

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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