David van der Spoel
spoel at xray.bmc.uu.se
Sun Nov 12 12:14:21 CET 2006
Paul van Maaren wrote:
> On Sunday 12 November 2006 10:42, Tsjerk Wassenaar wrote:
>> Probably someone will have a topology and a structure file for TFE
>> lying around (not me). But TFE isn't the worst of molecules and since
>> your new with Gromacs, I think it would be an excellent opportunity to
>> get acquinted with the program and force fields by parameterizing it
>> yourself. Find the paper of your favorite force field (choose one) and
>> check how the parameterization of the building blocks / molecules was
>> done. Take the same steps for TFE.
>> Maybe this isn't the answer you'd hoped for, but think of the saying
>> "give a man a fish and he can eat for a day; teach a man how to fish
>> and..." :)
> That's always a good approach, but for starters you might want to take a look
> at tfe.itp in the share/top directory.
... and check recent literature. IIRC there is a quite recent TFE model
for GROMOS-like force fields.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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