Force field for replica

From: Xiang Yu (yuxiang8057155_at_hotmail.com)
Date: Thu Oct 28 2010 - 09:12:25 CDT

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

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