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adding distance constrain between the centers of two molecules
Posted: Tue Nov 29, 2022 9:11 am
by qingyiyang
Hi, I'm new to OpenMM. Could someone help on adding distance constrain between the mass centers of two molecules? e.g.
f= k(r-ro)^a, r>r0
f=0,r<=r0
r is the distance between the centers of two molecules.
How should define the external force in openmm?
Thank you very much!
Re: adding distance constrain between the centers of two molecules
Posted: Tue Nov 29, 2022 10:11 am
by egallicc
Re: adding distance constrain between the centers of two molecules
Posted: Tue Nov 29, 2022 11:15 am
by peastman
The
API documentation on CustomCentroidBondForce may also be helpful. For your case an expression like this should work:
Code: Select all
force = CustomCentroidBondForce("k*max(0, r-r0)^a")
k, r0, and a can all be either global or per-bond parameters, whatever works for you. Or if they just have a single fixed value that never changes, you can just hardcode them in the expression:
Code: Select all
force = CustomCentroidBondForce("100*max(0, r-1.5)^2")
Remember that energies are in kJ/mol and distances are in nm.