[gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF

[David van der Spoel]

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>
> wrote:
> 
>> 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).
>>
> 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 
unphysical.


> BTW, meanwhile I found that the  [ implicit_genborn_params ] should come
> immediatly after the [ atomtypes ] section in topol.top file.
> 
> Regards,
> Alex
> 
>>
>>> %-------------TOP-----------
>>> #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
>>>
>>> Regards,
>>> Alex
>>>
>>
>>
>> --
>> 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.
>> http://www.icm.uu.se
>> --
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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.
http://www.icm.uu.se