VMD-L Mailing List

From: Rafael Bernardi (rcbernardi_at_auburn.edu)
Date: Sat Jan 16 2021 - 14:29:33 CST

Hello Tiglath,

Please next time send NAMD questions to the NAMD-L, not the VMD-L. That help us keeping things organized, and it is also where the NAMD users discus the problems they have with NAMD.

Answering your question. The file in question have the CHARMM 27 force field parameters for Proteins and Lipids. I wouldn’t say that that is the ideal parameter file to use anymore, newer versions of CHARMM are available and you should use those. The NAMD tutorial was created long ago, and newer tutorials, such as QwikMD or QM/MM, use CHARMM36 only. I would definitely recommend you using CHARMM36 parameter files.

To know more about the available CHARMM force field parameters, please visit: https://urldefense.com/v3/__https://www.charmm.org/charmm/resources/charmm-force-fields/__;!!DZ3fjg!rOpuMYTRr_1uVaG96ag3wX7P2fB99NWwPA2Th1fk0GTU6x6ew8d4IG-5jo4p4Hz9YQ$

Best wishes,

Rafael

……………………………………………………………………...
Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics
rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>
rcbernardi_at_ks.uiuc.edu<mailto:rcbernardi_at_ks.uiuc.edu>
http://www.ks.uiuc.edu/~rcbernardi>
+1 (334) 844-4393

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Tiglath Moradkhan <moradkhantig_at_gmail.com>
Date: Friday, January 15, 2021 at 7:23 PM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Question about NAMD configuration files

Hi VMD community

I have a quick question about the parameter files used in NAMD config files. In the NAMD configuration files used in the NAMD tutorial and in the sample.conf, the CHARM parameter file used is: par_all27_prot_lipid.inp. Is there a reason why this particle CHARM file is used? If not, then how can you tell which kind of parameter file should be chosen?

Thanks

Tiglath