RE: Running MD simulation for two molecules

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Apr 02 2019 - 12:14:33 CDT

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.

https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

-Josh



On 2019-04-02 00:29:59-06:00 owner-namd-l_at_ks.uiuc.edu 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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