[gmx-users] RE: multiple dihedrals

[Mark Abraham]

On 19/12/2010 11:13 PM, Jarmila Husby wrote:
> In amber dihedral parameters description, IDIVF is the factor by which the torsional barrier (Vn / or force constant) is divided.
> Usually, this number is 1, but in case of the "X" used in the dihedral definition like in the case bellow, where "X" stands for the actual atoms, such as atom1, atom2, atom3 and atom4, there are 3 combinations, giving IDIVF=3.

I still don't know what all the columns refer to, but GROMACS doesn't do 
any such gimmicky division... All I can suggest is that you write out 
the equations both programs claim to implement, and convert the 
parameters to the right units, and test a zero-step EM  for equivalence 
with both programs.

> What would be then the right set of entries for such a dihedral in gromacs 4.5?
>
> Jarmila
>
> On 18/12/2010 1:19 AM, Jarmila Husby wrote:
>>   Dear all,
>>
>> Could you please advise me on how to convert a dihedral amber
>> force-field parameter into amberport in Gromacs v 4.5? I have read the
>> mailing list and the manual, so I understand Gmx 4.5 can deal with
>> multiple entries per dihedral,

"multiple entries" refers to the way GROMACS mimics AMBER or CHARMM 
behaviour regarding accumulating dihedrals described by four specific 
atom types, usually of different multiplicity. So it's not relevant here.

Mark

>>   using the type 9 function, instead of
>> accumulating them into a single set of RB parameters.
>> But I do not know how to go about a dihedral with IDIVF number =3, and
>> wild-cards used in the dihedral definition, such as: X - CI - OS -
>> X    3   1.150    0.0   3.0
>> What would be the right set of entries for such a dihedral? All
>> suggestions would be much appreciated.
> What is an IDIVF?
>
> Mark
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