[gmx-users] Analytic first derivatives with respect to parameters?
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 13 20:31:13 CEST 2007
> Hi there,
> I'm trying to modify the GROMACS source code to obtain analytic
> derivatives of the energy and the force with respect to the force field
> parameters. The goal of this is to help improve force field fitting /
> optimization routines. Before I begin, has this already been done by
> anyone? If not, can someone give me a tip on where to actually declare
> the new variable (say, dE/dk where E is the energy and k is the force
- P. J. van Maaren and D. van der Spoel: Molecular Dynamics Simulations
of Water With Novel Shell-Model Potentials J. Phys. Chem. B. 105 pp.
- David van der Spoel, Paul J. van Maaren and Herman J.C. Berendsen: A
systematic study of water models for molecular simulation: Derivation of
water models optimized for use with a reaction field. J Chem Phys 108
pp. 10220-10230 (1998)
in addition there is a bit more along these lines in the program ffscan
but not exactly what you are indicating.
On the other hand FEP calculations do compute these, for instance
changing a force contant from A->B you will get the analytical energy
derivative. See manual and relevant references therein.
> Thanks a lot!
> - Lee-Ping Wang
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users