Re: Force field for replica

From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Oct 31 2010 - 08:47:09 CDT

CMAP parameters are either in the forcefield file(s) you're using or they're
not. See: http://mackerell.umaryland.edu/CHARMM_ff_params.html

Best,
Chris

2010/10/28 Xiang Yu <yuxiang8057155_at_hotmail.com>

> Hi everyone,
>
> I want to use replica exchange with NAMD. I checked the example included in
> NAMD and found a problem of the force field. The force field of the example
> comes from Charmm19. Bond, angle, dihe are added into the beginning of each
> line and ŠĆ is positive one. I can not figure out why these modification is
> required.
>
> I want to do the simulation with Charmm27 force field. So I have to
> generate a force field with the parameters of bond, angle, dihe, impr,
> nonbonded and CMAP. But how to put CMAP parameters in this special force
> field for REMD? I tested a REMD simulation with a force field without CMAP
> parameters. An fatal error will come out which tell me the cross term
> parameters are missing.
>
> So does anyone know how to add CMAP into a force field for REMD or how to
> let namd skip CMAP during simulaiton?
>
> Thank you,
>
> Xiang
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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