[Fwd: Re: Using CHARMM27]

From: Victor Ovchinnikov (ovchinnv_at_georgetown.edu)
Date: Wed Jun 20 2007 - 11:49:36 CDT

attached mail follows:


1) NAMD supports XPLOR psf format only.
2) None. CHARMM is a separate software package. NAMD, however, can use
CHARMM parameter files. There are the three types that you listed.
They can be obtained from Alex MacKerell's website at the University of
Maryland. You will be using the CHARMM27 forcefield for your NA
simulations.

N.B. I case you are confused, CHARMM is _not_ the same as charm++.
charmm++ is a parallel communication library that NAMD uses.

Victor

On Wed, 2007-06-20 at 09:48 -0500, Audrey Salazar wrote:
> 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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