[gmx-users] New force fields

David van der Spoel spoel at xray.bmc.uu.se
Fri May 3 16:18:06 CEST 2002

On Fri, 3 May 2002, Ram'on Garc'ia Fern'andez wrote:

>> For generating starting conformations I would think LJ with softcore would 
>> be quite pain-free. 
>But at present, it is almost imposible to do LJ with softcore.
It's two parameters in the mdp file. Set sc_alpha to e.g. 1.5
; Free energy control stuff =
sc-alpha                 = 0
sc-sigma                 = 0.3

then you blow up the box by a factor of say 1.5, minimize, and do softcore 
MD with pressure coupling.

>Gromacs should document how to add a custom potential by formula to
>the source code, and allow with a reasonable amount of paramenters (such as
>four). It was straightforward with DLPOLY, I just modified forgen.f.

I agree we could have more documentation, but that costs time as well...

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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