[gmx-users] Implicit solvent simulation

Edgar Luttmann luttmann at stanford.edu
Thu Jul 19 10:15:16 CEST 2007

Hi Erik,

Erik Lindahl wrote:
> Hi,
> On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
>> The version used by Alan Mark has never made it into gromacs. Rather, 
>> Erik Lindahl started the implementation of this stuff but did never 
>> finish it completely, due to other priorities I presume. We should 
>> however take out the variables to avoid confusion (unless someone 
>> provides a full implementation).
> Actually, technically the GB implementation is already in Gromacs (even 
> assembly kernels), and quite correct, it's just that you don't have the 
> born radii yet :-)
I can't find any usage of the GB parameters as read from the mdp file - 
neither in the latest release nor the HEAD revision in the CVS. Is there 
another branch in the CVS you got that code in?
I'm just curious as we worked on some GB models as well and using (at 
least the STILL) with assembly loops sounds very nice to me.

Somewhat unrelated: I also saw the andersen_seed parameter and I was 
wondering if there is a code branch that contains an Andersen thermostat?


Edgar Luttmann, PhD

Stanford University, Stanford, CA, USA
Department of Chemistry, Group of Prof. Dr. V. Pande
postdoctoral researcher: Folding at home - distributed computing

Clark Center, 94305-5080 Stanford, CA, phone: (650) 723 1097
email: luttmann AT stanford.edu, www: http://www.stanford.edu/~luttmann

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