Re: membrane equilibration

From: Ajasja Ljubetič (
Date: Fri Mar 04 2011 - 05:09:19 CST

Dear Jeremy,

I have prepared some systems using CHARMM-GUI. I found it simplest to
equilibrate in CHARMM and run the production using NAMD. (The CHARMM-GUI
scripts use a lot of restraints during equlibration. The same restraints
could probalby also be implemented in NAMD usin the excellent colvar module,
but I never took the time).
When switching to NAMD I found it easiest just to rebuild the psf and start
from there. An example script is attached. It splits the PDB to segments,
builds the PSF and writs a NAMD compatible PSF.

Best regards,

On Fri, Mar 4, 2011 at 01:30, jeremy adler <> wrote:

> Hi Dir. Harrison,
> these are the last few lines of minimization (1000 steps with virtually no
> change in the energies. If the equilibration in charmm was carried out over
> about 1500ps behaved itslef perfectly well in the subsequent production
> run.. As potentially another solution, do you know of a script that will
> convert charmm restart files into namd restart files?
> thanks!

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