How parameters are assigned in OpenMM?

[Robin Singh]

Hi OpenMM developers,

I have a query regarding the assigning of parameters by OpenMM from the force field (.xml) file to the input (.pdb) file. I am working on an aqueous KCl solution using tip3p force field (the files are attached below). The calculation is running fine but I don't know how assigning of parameters are taking place. In the force field file, the atom name is defined as K and CL and their standard atom types are written as K+ and Cl- respectively. In my input file, the atom name and residue name are written as K+ (both) and Cl- (both). There is no atom type is written but for assignment of parameters, the things should match exactly right?. I have looked in the manual as well but I could not find any concrete answer.

I am doing some NVT calculations and they are running fine and whenever I remove any parameter (regarding K+ and Cl-) from the .xml file, I get an error. But the problem is...on what basis the assignment of parameters is taking place. On the working part, things are fine but on the understanding part, I am having some issues.

It will be very nice of you if you could explain how OpenMM assign parameters from the .xml file to the .pdb file.

Note: .pdb extension was not allowed to attach here, so I converted that to .txt extension and have attached here.

Regards,
Robin Singh

[Peter Eastman]

The force field format is documented at http://docs.openmm.org/latest/userguide ... g_ffs.html. Atom types are assigned based on elements and bonds. It doesn't matter what names the atoms have, so long as the element symbol column is filled in correctly.

[Robin Singh]

Thank you so much for the reply.

Regards,
Robin