[gmx-users] Amber Force field in Gromacs - implicit solvent

David spoel at xray.bmc.uu.se
Sun Oct 20 07:12:30 CEST 2002

On Sat, 2002-10-19 at 13:46, Stefano Piana wrote:
> Hallo again!
> I would like to know the current status of the implementation of the Amber 
> forcefield in gromos. I Read some old messages on the argument, does it 
> already exist a version of the Amber force field written in gromacs format?
The Pande group (folding.stanford.edu) have implemented both Amber and
Charm in GROMACS. It is currently being tested. As soon as they are
convinced that it works we will add it to the standard distribution.

> In the meantime ma and Alessandro Laio have written a small program to convert 
> Amber topologies and coordinates into Gromos and Gromacs topologies and 
> coordinates. It is still a bit experimental (i.e. not extensively tested), but 
> it seems to work fine. Let me know if this could be of interest to somebody.
If you can do as a test both a protein in water, and DNA in water it
would be useful. There must be plenty of Amber topology files out there.
If you think that it works well you can upload it to the gromacs website
(under contributions).

> Finally I would like to know if there is any project to incorporate some kind 
> of implicit solvent model in gromacs.
Also the Pande group together with Erik Lindahl have done this. Don't
know about the status of this.

> Thanks for your answers!
> Stefano
> -- 
> ETHZ Honggerberg - HCI H203
> 8093 Zurich, Switzerland
> Tel: +41 1 6323054
> Fax: +41 1 6321090
> piana at inorg.chem.ethz.ch
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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