[gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF

Discussion:

Alex

2018-12-04 20:58:49 UTC

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.

%-------------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

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David van der Spoel

2018-12-04 21:23:36 UTC

Permalink

Post by 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.

Post by 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

Alex

2018-12-04 21:49:37 UTC

Permalink

Hi David,
Thank you.

Post by Alex

implicit_genborn_params ]

Post by Alex
parameters are in a gbsa.itp file but that was not the case for

Gromos54a7

Post by Alex
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 ... .

Post by Alex
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.

BTW, meanwhile I found that the [ implicit_genborn_params ] should come
immediatly after the [ atomtypes ] section in topol.top file.

Regards,
Alex

Post by 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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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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* For (un)subscribe requests visit
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David van der Spoel

2018-12-06 10:07:30 UTC

Permalink

Post by Alex
Hi David,
Thank you.

Post by Alex

implicit_genborn_params ]

Post by Alex
parameters are in a gbsa.itp file but that was not the case for

Gromos54a7

Post by Alex
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 ... .

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.

Post by Alex
BTW, meanwhile I found that the [ implicit_genborn_params ] should come
immediatly after the [ atomtypes ] section in topol.top file.
Regards,
Alex

Post by 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