[gmx-users] forcefield.itp file for gromos45a3 and oplsaa
yujan2007 at gmail.com
Wed Jan 4 17:33:20 CET 2012
Got it, Thank you, Mark!
On Wed, Jan 4, 2012 at 1:18 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 4/01/2012 4:43 PM, XUEMING TANG wrote:
>> 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.
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