[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...
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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