[gmx-users] Non-bonded parameters in Gromacs

[Anton Feenstra]

Marc Baaden wrote:
> 
> Hi,
> 
> I need to introduce new atomtypes/parameters in Gromacs for my
> current project (ie for Fe3+, which in the standard version has
> zero VDW parms). Now after going through manual and online help
> I think I got a rough picture but some things remain unclear.
> 
> 1) Eg. let's say I use Fe parameters from another forcefield and
> transform them into C6/C12 values, do I need to generate all
> possible combinations with other atom-types and add them as well
> (as in all forcefields that come with Gromacs the GenPairs option
> is set to No, and I think there can only be one defaults section
> in the topology) ?
> 
> If so, are there any tools available (scripts, ..) ?
> 
> 2) BTW, if there are no LJ parameters for a given pair and one uses
> GenPairs=No, will there be an error message, or will they be set
> to zero implicitly (in which case entries like
>    FE   OD    1 0.00000E+00   0.00000E+00
> are superfluous).

GenPairs, if I'm not mistaken, is for LJ 1-4 interactions (see p97).

> 3) In the case that I create a complete new forcefield (based eg on
> previous work with Amber), wanting to use GenPairs=Yes, what do
> the FudgeLJ and FudgeQQ parameters do ??
> (Are these two parameters what is called scaling factors for
> LJ/Coulomb interactions in other forcefields ? - it's just because
> I would have expected those in the mdp rather than in the parameters ..)

What they say they do on page 98.

> 4) Is there a tool that allows to get a list of the parameters actually
> used in a simulation .. that is more human readable than a
> gmxdump -s tprfile ?

I've posted a rudimentary topology parsing script to the list some
time ago, search for 'topology parsing' on www.gromacs.org/search
or go to: hwww.gromacs.org/pipermail/gmx-users/2001-December/000373.html

I've used this to prepare a table to describe the complete forcefield of 
a molecule. This table I included as suplementary material to an
article.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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