On 2012-02-21 23:26, Broadbent, Richard wrote:
On 21/02/2012 19:02, "David van der Spoel"<sp...@xray.bmc.uu.se> wrote:
On 2/21/12 6:17 PM, Richard Broadbent wrote:
Dear All,
I am considering conducting a simulation of a polymeric system in
gromacs. I would like to use the COMPASS forcefield as it has a complete
parameter set for my molecule.
I believe the majority of the implementation is simple (though long and
fiddly). However, it has Bond-Dihedral and Angle-Dihedral cross terms.
These terms are not listed in either Chapter 4 or 5 of the Manual. Which
leads me to believe that they are not implemented. However CMAP
dihedrals are not documented in chapters 4& 5 and they are implemented
in the code. I therefore had a quick look in src/gmxlib/ifunc.c and
couldn't see those terms. However, my knowledge of the layout of the
source code is extremely limited so I could be looking in the wrong
place, and thought it best to ask.
Are Bond-Dihedral and Angle-Dihedral cross terms available in gromacs
4.5.5?
What do the functions look like?
Bond dihedral:
(b-b0)*[k_1*cos(phi) +k_2*cos(2*phi)+k_3*cos(3*phi)]
Angle Dihedral:
(theta -theta_0)*[k_1*cos(phi) +k_2*cos(2*phi)+k_3*cos(3*phi)]
There is also angle-angle-dihedral:
k*(theta -theta_0)*(theta' -theta_0')*cos(phi)
For this to work, the best would be to implement a new dihedral
function. Due to the way this works the function would need quite a few
parameters though.
atoms i,j,k,l
3 b0 for i,j and j,k and k,l
2 theta_0 for i,j,k and j,k,l
k_1, k_2, k_3 (shouldn't there be a k_0)?
In all 8-9 parameters! What also is unfortunate is that a number of
these parameters are most likely repeats (b0, theta_0) from other lists.
One could of course combine bonds, angles and dihedrals into one monster
routine, but then dealing with constraints becomes somewhat harder again.
By the way this thread now should be moved to the developer list I guess.
Most likely they are not implemented though if they're not in the manual.
Thanks,
Richard
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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