How parameters are assigned in OpenMM?
Posted: Mon Jun 19, 2023 12:50 am
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
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