Using CHARMM27

From: alsalazar_at_northwestern.edu
Date: Wed Jun 20 2007 - 10:27:53 CDT

('binary' encoding is not supported, stored as-is) Hello,
I am a first year graduate student trying to understand and run the CHARMM27 force field using NAMD
(I will be simulating nucleic acids). As I familiarize myself with NAMD, I find that I have
several unanswered questions that I am hoping someone would be willing to answer. I am listing
them below.

1) From the webpage below, I am gathering that PSF files in XPLOR or CHARMM formats will run in
NAMD as a CHARMM MD simulation. Is this the case?

http://www.ks.uiuc.edu/Research/namd/2.6/ug/node13.html#SECTION00061300000000000000
2) I installed NAMD 2.6 from source code and CHARMM was installed with it. The webpage above
states that CHARMM19, CHARMM22, and CHARMM27 file formats are supported by NAMD. How many versions
of the CHARMM force field are included by default in NAMD 2.6? I.e., how do I know which version of
CHARMM I am using for my MD simulation?

Thank you in advance.

Audrey Salazar

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA

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