simtk.org

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

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.

Thank you so much for the reply.

Regards,
Robin