[gmx-users] CHARMM force field implementation in Gromacs :
Nicolas SAPAY
nsapay at ucalgary.ca
Thu Sep 14 19:37:44 CEST 2006
Thanks for your answers (I had forgotten this comment in the script).
The problem is that most of dihedral with multiplicity n >= 6 don't come
alone. For exemple in Arg :
HD1 HE
| | | //
--CG--CD--NE--CZ
| | \
HD2
is defined by 6 dihedral with n>=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ)> They
are all of the same type (X-CT2-CT2-X). So, if I understand well, the
result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are
not a combination of different type of dihedrals with n >= 6.
The problems happen when a combination of different types of dihedral are
used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type
B). In this case, one possibility is to hack the Gromacs code by allowing
a 6th Ryckaert-Bellemans parameter (?)
Cheers
Nico
>> Hello,
>>
>> I have noticed that both in the Yuguang Mu's and the Mark Abraham's
>> work,
>> the periodic parameters of dihedral angles have been converted into
>> Ryckaert-Bellemans ones. I have tried to find more info about this in
>> the
>> CHARMM and Gromacs documentations but I have not found much. Why
>> exactly
>> this conversion should be done since the periodic potential is
>> implemented
>> in both force fields? My problem is that several dihedral angles cannot
>> be
>> easily converted in RB parameters since their multiplicities is equal to
>> 6
>> and the RB potential implemetation is limited to 5 constants.
>
> To quote my own code comment,
>
> "# We need some elaborate functionality to convert the CHARMM dihedral
> type
> # of k * (1 + cos(n * xi - delta ) ) functions summed over n into
> something
> # GROMACS can implement. While the above functional form exists in
> # GROMACS, you can't have more than one function of this type, and
> # CHARMM has a number of dihedral interactions that require more than
> # one such function. However for delta = 0 or pi and n <= 5, then the
> above
> # cosine function can be expanded in powers of cos xi, and the
> coefficients
> # of the expansion can be summed in this conversion and presented to
> # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this
> # works because CHARMM only uses such delta and n values for atom type
> # combinations that need multiple functions of the above form. Warnings
> # are issued when delta is some other value, and the algorithm dies if
> # n is > 6. In order to simplify GROMACS logfile output so that it only
> # has to report one sort of dihedral term for most simulations, all
> # dihedral terms with n <= 5 are expressed as R-B, even when not
> necessary.
> # Dihedrals with n=6 are left in periodic form, since it is not possible
> # to convert these to R-B form when the summation is limited to the
> # fifth power of cos xi."
>
> So if you have a single dihedral over a set of atoms that has n>=6 then
> you can leave it in periodic form and the only cost is that you have to
> remember that the output will likely have both periodic and R-B
> dihedrals.
> If you have one such a dihedral in combination with others n<6 then you
> can use a combination of periodic and R-B. If you have multiple dihedrals
> with n>=6 you will need to hack the source code, except in some trivial
> cases, perhaps.
>
> Mark
>
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