[gmx-users] forcefield.itp file for gromos45a3 and oplsaa

[Mark Abraham]

On 4/01/2012 4:43 PM, XUEMING TANG wrote:
> Hello
>
> I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) 
> and also in Gromos (C6 and C12) forcefield for comparison. The 
> original ffnonbonded.itp file in oplsaa.ff has no pair potential 
> listed. While the original ffnonbonded.itp file in gromos**.ff listed 
> all the pair potentials. If I change one atom potential, do I need to 
> do anything to generate the new pair potential before running a 
> simulation in opls-aa force field? Or how to generate the pair 
> potentials? While for the case of gromos forcefield, the 
> forcefield.itp file shows no pair potential will be generated. Is 
> there any automatic ways to generate the modified LJ potentials? 
> Should I list every possible LJ pair potentials in nonbonded.itp file? 
> It looks like some very tedious work if several atoms are going to be 
> modified.
> Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? 
> Values of those two are different for OPLS and Gromos.

In general, two force fields work differently and have their own 
idiosyncrasies that will show up in how GROMACS implements them. When 
modifying them, you should be sure to check the original literature and 
the GROMACS manual and satisfy yourself how your changes will work. You 
should search the manual for discussion of the use of gen-pairs and the 
fudge values. I don't know why the list of [ nonbond_param ] values is 
exhaustive - you'd think the combination rules could be used. In 
practice, you only need to add parameters for interactions that can 
occur in your system, and grompp will complain about those that it can't 
find.

Mark