Force field for coarse grained simulations (and other questions)

From: patrick wintrode (pat_wde2_at_yahoo.com)
Date: Wed Jul 11 2007 - 16:20:20 CDT

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Hi.

I want to set up a CG simulation using the residue based coarse graining tools that are included in the latest version of VMD.

In the paper I read (the virus simulation by Arkhipov in Structure, 2006) it said that a "CHARMM style force field" was used. Does anyone have more details on this, or know where it can be obtained?

Also, is there a common choice for cutoff distances and timesteps for residue based CG simulations, or do the need to be chosen on a case by case basis?

Finally, does someone have a sample .conf file for CG simulations (like the samples available for standard NAMD simulations)?

Thanks.

Patrick L. Wintrode
Assistant Professor
Dept. of Physiology & Biophysics
Case Western Reserve University
Cleveland, Ohio 44106

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