Thank you.
This means I can infer the values from the Parameter and Topology CHARMM files,
right?
Best regards,
Stephan
Thank you.
This means I can infer the values from the Parameter and Topology CHARMM
files,
right?
i don't *know*, i only vaguely remembered a cyclic structure issue from
the discussion with josh last fall.
so i had a look at example and benchmark data files in LAMMPS: they only
have weights of 1.0, 0.5 and 0.0.
and i had a look at the comments in topogromacs.tcl in the topotools
package from which i inferred the rest.
if i knew for certain, i would have said so.
Dear LAMMPS uses,
dear Axel,
thanks a million!
I could accomodate my implementation.
I'm sorry I had to assure before adapting
the code, thus I apologize for inquiring further.
Best regards,
Stephan
Dear LAMMPS uses,
dear Axel,thanks a million!
I could accomodate my implementation.I'm sorry I had to assure before adapting
the code, thus I apologize for inquiring further.
i've looked at the LAMMPS documentation and found it rather vague in this
respect, so i've rewritten it somewhat, in the hope to avoid confusion in
the future:
The weighting factor is required to correct for double counting
pairwise non-bonded Lennard-Jones interactions in cyclic systems
or when using the CHARMM dihedral style with non-CHARMM force fields.
With the CHARMM dihedral style, interactions between the 1st and
4th atoms in a dihedral are skipped during the normal non-bonded
force computation and instead evaluated as part of the dihedral
using special epsilon and sigma values specified with the
"pair_coeff"_pair_charmm.html command of pair styles that
contain "lj/charmm" (e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html)
In 6-membered rings, the same 1-4 interaction would be computed
twice (once for the clockwise 1-4 pair in dihedral 1-2-3-4 and
once in the counterclockwise dihedral 1-6-5-4) and thus the
weighting factor has to be 0.5 in this case.
In 4-membered or 5-membered rings, the 1-4 dihedral also is
counted as a 1-2 or 1-3 interaction when going around the
ring in the opposite direction and thus the weighting factor
is 0.0, as the 1-2 and 1-3 exclusions take precedence.
Note that this dihedral weighting factor is unrelated to the
scaling factor specified by the "special bonds"_special_bonds.html
command which applies to all 1-4 interactions in the system.
For CHARMM force fields, the special_bonds 1-4 interaction scaling
factor should be set to 0.0. Since the corresponding 1-4 non-bonded
interactions are computed with the dihedral.
This means that if any of the weighting factors defined as dihedral
coefficients (4th coeff above) are non-zero, then you must use a
pair style with "lj/charmm" and set the special_bonds 1-4 scaling
factor to 0.0 (which is the default). Otherwise 1-4 non-bonded
interactions in dihedrals will be computed twice.
For AMBER force fields, which use pair styles with "lj/cut",
the special_bonds 1-4 scaling factor should be set to the AMBER
defaults (1/2 and 5/6) and all the dihedral weighting factors
(4th coeff above) must be set to 0.0. In this case, you can use
any pair style you wish, since the dihedral does not need any
Lennard-Jones parameter information and will not compute any
1-4 non-bonded interactions.
Dear Axel,
thanks, this clarifies what I've read
previously in the documentation.
Best,
Stephan