[gmx-users] Implicit solvent simulation

[Moore, Jonathan (J)]

I asked for and received the code a couple of years ago.

As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges.  Also, the different models (Still, etc.) are
implemented in independent versions of the code.  Also, the GB part is
actually implemented in FORTRAN.   


Jonathan

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-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Ran Friedman
Sent: Wednesday, July 18, 2007 10:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Implicit solvent simulation

Dear Tom,

The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.

Ran.

TJ Piggot wrote:
> Hi,
>
> Just to let people know in case they are unaware there is a paper
> where implicit solvent models have been implemented in GROMACS, the
> paper can be found using the following link:
>
>
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid
=15814616
>
>
> Tom
>
> --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>
>> SeungPyo Hong wrote:
>>> Thank you for your kind reply, Stephane.
>>> Anyhow it is a little disappointing that Generalized-Born is not
>>> implemented in Gromacs.
>>>
>>
>> I've put it on the development TODO list (feel free to volunteer)
>>
>> http://wiki.gromacs.org/index.php/Implicit_Solvent
>>
>> The reason it is not there is because none of the developers has
>> considered it worthwhile.
>>
>> -- 
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax:
>> +4618511755.
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> _______________________________________________
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>
>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
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-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
------------------------------------------------------

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