[gmx-users] ffscan trouble
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 10 17:00:29 CEST 2006
Zlenko Dmitry wrote:
> Well, I have a lipid bilayer whith unusual composition and unusual
> lipids (whith irregular head groups). It's possible to calculate a
> strength constant as second partial derivatives of full energy by
> an apropriate coordinates (accordig, for example, to GAMES or PC
> GAMES software). But, as I read, there are another more accurate
> way, based on minimisation of disagriments between mechanical
> potential energy surface and QM one:
this is beyond the capabilities of ffscan. you'll have to check
literature on parameterization for your favorite force field.
> AFMM: A molecular mechanics force field vibrational
> parametrization program. A.C. Vaiana 1, Z. Cournia, I.B. Costescu,
> J.C. Smith. C.P.C. 167,34-42 (2005).
> A quantum mechanical polarizable force field for biomolecular
> interactions. A.G.Donchev, V.D.Ozrin, M.V.Subbotin, O.V.Tarasov,
> and V.I.Tarasov. PNAS 102,7829-34 (2005);
> Derivation of force fields for molecular mechanics and dynamics
> from ab initio energy surfaces. J.R.Maple, U.Dinur, and
> A.T.Hagler. Proc. Nati. Acad. Sci. 85,5350-54 (1988).
> So, could ffscan help me or not?
> Thank you for your attention,
> Zlenko Dmitry.
> Biophysical subdivisoin of
> Biological faculty of Moscow State University.
> Moscow, Russia.
> d_zlenko at mail.ru
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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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