Re: Selectively turning off electrostatic interactions

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Mar 11 2009 - 15:28:46 CDT

Greddy,

Can you please explain why you want to do this, particularly with an entire protein? This will not provide an accurate free-energy of solvation which some people have naively suggested before. Leaving the vdW potentials in full effect without electrostatics will result in aberrant dynamics that will propagate through your system with time leading to large inaccuracies. If you're lucky, the simulation will simply crash with velocity exceptions after several timesteps.

C.

--
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
govardhan reddy <greddy1_at_umd.edu> writes:
> Date: Wed, 11 Mar 2009 12:36:57 -0400
> From: govardhan reddy <greddy1_at_umd.edu>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Selectively turning off electrostatic interactions
> Return-Path: char_at_halifax.ks.uiuc.edu
> Message-Id: <69F5EBCD-A786-490B-8769-DFDB87778E30_at_umd.edu>
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> 
> Hello all,
>
> I have a protein solvated in water. I just want to turn off protein- 
> water electrostatic interactions but keep the protein-protein and  
> water-water electrostatic interactions intact.  If anybody has performed 
> such kind of calculations in NAMD or in any other package before, I will 
> be grateful if you can provide me any input.
>
> Thanks
> Greddy
>

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