Queries regarding CustomNonbondedForce

[Robin Singh]

Hello,

I want to perform CustomNonbondedForce calculations for an aqueous solution of salt. I want to apply customization only on the ions of the salt and not on the water molecules. So during my calculation, I defined a CustomNonbondedForce and gave parameters for the ions (parameters in the NonbondedForce section for the ions were kept 0) and I kept the parameters of O and H atoms of water molecule in the NonBondedForce section only. But I got the below mentioned error:

"ValueError: CustomNonbondedForce: No parameters defined for atom type tip3p-O"

If I put O and H parameters in the CustomNonbondedForce section then everything is working fine.

I want to ask is there any way in OpenMM that can let me to use CustomNonbondedForce on some components of my system and I can use the normal NonbondedForce on the other components?

Regards,
Robin Singh

[Peter Eastman]

NonbondedForce and CustomNonbondedForce both define interactions of every particle in the system with every other. That means you need to define parameters for every particle. It's ok if some of those parameters are such that they don't actually interact, such as having a charge of 0. But you do need to define what the parameters are.

Can you describe what you're trying to accomplish? In what way do you want to customize the ions? There may be a better way of doing it.

[Robin Singh]

Thanks for your reply Peter. As I mentioned earlier, I want to try customization on ions only (means I want to try new functional forms and corresponding parameters only on the ions of the salt) and keep everything for H and O of water molecules as such as they are defined for tip3p. I tried to put epsilon for O as 0 in CustomNonbondedForce (and parameters for O in NonbondedForce were kept as such) but the results are way off for aqueous salt solution and are near to the case when I would have only the salt in the pdb. It just processed the salt and completely ignored the water molecules.

Can anything else be done that OpenMM process both, salt and water but salt with CustomNonbondedForce and water with NonbondedForce ?

Regards,
Robin Singh