Re: Selectively turning off electrostatic interactions

From: govardhan reddy (greddy1_at_umd.edu)
Date: Wed Mar 11 2009 - 15:57:33 CDT

Hello Chris,
I have a layer of water trapped between two domains of the protein
preventing the collapse of the domains. I believe electrostatic
interactions between the protein and water are responsible for this
metastable state. I want to see whether the collapse of the domains
will accelerate or not if I switch off these interactions.
Thanks
G. Reddy

On Mar 11, 2009, at 4:28 PM, Chris Harrison wrote:

> 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>
>> X-Spam-Status: No, score=-2.6 required=5.0 tests=AWL,BAYES_00
>> autolearn=unavailable version=3.1.7-0+tcb1
>>
>> 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
>>
>

***************************************************
Govardhan Reddy
Research Associate
Institute for Physical Science and Technology
University of Maryland-College Park
College Park, MD - 20742
Phone: +1-301-405-4822
Fax: +1-301-314-9404

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:48 CST