[gmx-users] Non-bonded parameters in Gromacs

[Marc Baaden]

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).


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 ..)


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 ?


Cheers,
  Marc

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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