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
| | | //
--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
You can add multiple dihedrals with identical atoms in the top file,
don't know about the rtp file.
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David.
________________________________________________________________________
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
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