[gmx-users] Continuum solvent

Tom Joseph tom-lists at jambon.ll.cx
Thu Apr 6 02:00:19 CEST 2006

The authors of the following paper implemented Generalized Born in  
GROMACS.  They seem willing to send their modifications to people who  
email them and ask.

Comparative study of generalized Born models: protein dynamics.  Proc  
Natl Acad Sci U S A. 2005 May 10;102(19):6760-4. Epub 2005 Apr 6.


On Apr 5, 2006, at 7:17 PM, Ashutosh Jogalekar wrote:

> Hi
> Is there any way at all to do an implicit solvent simulation in  
> Gromacs? I am trying to do an in vacuo minimization, but the  
> structure is blowing up and getting highly distorted. I am guessing  
> it is because of the overwhelming electrostatic interactions in  
> vacuum. So I want to use a continuum solvent model to do this if I  
> can. I could use another program, but then it may not be a  
> 'controlled experiment'
> Thanks
> Ashutosh Jogalekar
> Emory University
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