Re: Running MD simulation for two molecules

From: 김민재 (
Date: Wed Apr 03 2019 - 01:44:46 CDT

I actually ended up using "readpsf+writepsf" though.

On Wed, Apr 3, 2019 at 2:14 AM Vermaas, Joshua <>

> No. NAMD assumes you have a single psf/pdb pair that includes your whole
> system. Merging the systems together in VMD *should* be fairly easy to do.
> If the individual parts are simulatable, the "mergemols" command from
> topotools will do what needs to be done.
> -Josh
> On 2019-04-02 00:29:59-06:00 wrote:
> Hi everyone,
> I am currently trying to run a simulation for two molecules (1ca2 and its
> inhibitor AZM.) I have pdb and psf files for both 1ca2 and AZM, and was
> wondering if I had to combine those two into one pdb and psf file to run a
> MD simulation on NAMD. If it were possible to set two structures in my
> configuration file would I just write two lines for structure and
> coordinates? (I am asking because VMD is having a problem combining the
> coordinates of 1ca2 and AZM, but that is not part of my question for this
> post...)
> Thanks!

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