[gmx-developers] Bond-angle coupling

MURAT OZTURK murozturk at ku.edu.tr
Thu Oct 4 14:28:17 CEST 2012


I am thinking about hacking gromacs in the following way :

I would like to have an angle potential that would turn on/off depending on
the energy of a particular bond.

For example, I will have a lennard-jones-cosine potential for a bonded
interaction. This will continuously go to '0' at a threshold. Then I will
have an angle potential between these two atoms (and a third one).

For each calculation, I would like the angle potential to be multiplied by
the instantaneous value of the bond potential, effectively turning it off
if the bond is 'broken'.

This is to represent a hydrogen bond in a coarse grained model.

I have intermediate C/C++ skills (that I haven't used in a while), but I am
intimidated by the parallel nature of the code and am not familiar with the
internals of gmx. I am willing to work on this full time for a week or so.

I would truly appreciate if someone could comment on the feasibility of
this hack, and possibly show me where to begin.

Thank you

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