[gmx-users] CHARMM force field implementation in Gromacs :
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 14 22:02:28 CEST 2006
Nicolas SAPAY wrote:
> 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
> | | | //
> | | \
> 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 (?)
>>> I have noticed that both in the Yuguang Mu's and the Mark Abraham's
>>> the periodic parameters of dihedral angles have been converted into
>>> Ryckaert-Bellemans ones. I have tried to find more info about this in
>>> CHARMM and Gromacs documentations but I have not found much. Why
>>> this conversion should be done since the periodic potential is
>>> in both force fields? My problem is that several dihedral angles cannot
>>> easily converted in RB parameters since their multiplicities is equal to
>>> 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
>> # of k * (1 + cos(n * xi - delta ) ) functions summed over n into
>> # 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
>> # cosine function can be expanded in powers of cos xi, and the
>> # 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
>> # 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
>> 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.
You can add multiple dihedrals with identical atoms in the top file,
don't know about the rtp file.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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