[gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 6 11:07:16 CET 2018
Den 2018-12-04 kl. 22:49, skrev Alex:
> Hi David,
> Thank you.
> On Tue, Dec 4, 2018 at 4:24 PM David van der Spoel <spoel at xray.bmc.uu.se>
>> 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
>>> 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).
> I didn't know that, I use the 2018.2 version and at least the tpr file can
> be produced ... .
>> 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.
> If non of Still, HCT and OBC, then what else you would suggest that has
> been implemented in Gromacs and could be used easily in Gromacs?
> I just wanted to see the diffusion and adsorption of some polymers to solid
> surface. The process is so slow in explicit water and I just wanted to see
> it the polymer come to the surface at all! However I see too much force in
> the slab with the current [ implicit_genborn_params ] parameter which I
> have used for now.
For qualitative work it is fine, although there is basically no
correlation between explicit solvent and implicit solvent for solvation
energies (e.g. J. Chem. Theory Comput. 13 pp. 1034-1043 (2017)). This
means that even if your polymer adsorbs to the surface, it may be
> BTW, meanwhile I found that the [ implicit_genborn_params ] should come
> immediatly after the [ atomtypes ] section in topol.top file.
>>> #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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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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