[gmx-users] CH1 vs. CS1, advice on silanol angles and dihedrals

[Anton Feenstra]

Sherwin J. Singer wrote:
> I would appreciate help with force field constructions:
> 
> 1) beta-D-glucose:

Don't know much about sugars and/or prodrg...

> 2) Silanols at a silicate surface (diagram below might only look right
> with fixed width font):
[...]
> * Approximate OS-SI-OA by OS-SI-OS, which can be found in ffgmxbon.itp?
> * Approximate SI-OA-OH by SI-OS-Si?
> * Approximate *-SI-OA-* dihedral by *-SI-OS-* dihedral?

That all seems pretty reasonable. See if you would have any 'experimental'
results (or literature data) you could compare against. Otherwise, doing
ab-initio is the only sensible basis for adjusting these parameters

> I also have a question about how your convention for dihedrals:
[...]

As it says in the manual, the gromacs forcefield (as well as the Gromos,
by the way), define only one potential for each rotatable bond.



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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