[gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF
David van der Spoel
spoel at xray.bmc.uu.se
Tue Dec 4 22:23:40 CET 2018
Den 2018-12-04 kl. 21:58, skrev Alex:
> Dear all.
> I wonder where the [ implicit_genborn_params ] section should come in the
> below topol.top file for which the Gromos54a7 force fields are used?
> For the Amber and OPLS-FF I notice that all the [ implicit_genborn_params ]
> parameters are in a gbsa.itp file but that was not the case for Gromos54a7
> and even it did not worked when I created a gbsa.itp for for gromos5a7.
Please note first that only the 4.5 and 4.6 branches of gromacs run
generalized born efficiently and reliably (as far as I know).
Second, if there is no predefined force field you should not make an
ad-hoc one but use a well-defined one instead.
Third, why bother with generalized born at all? There are so many papers
showing that the predictive power is poor that it will be hard to defend
any results based on it.
> #include "/u/alex/.local/gromos54a7.ff/forcefield.itp"
> #include "A.itp"
> #include "B.itp"
> #include "C.itp"
> [ system ]
> A-B-C in implicit water
> [ molecules ]
> A 1
> B 29
> C 14
> B 29
> C 14
> Thank you
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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