[gmx-users] COMPASS force field revisited Bond Dihedral and Angle Dihedral cross terms

Broadbent, Richard richard.broadbent09 at imperial.ac.uk
Tue Feb 21 23:26:00 CET 2012

On 21/02/2012 19:02, "David van der Spoel" <spoel at 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)

> Most likely they are not implemented though if they're not in the manual.

>> Thanks,
>> Richard

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