Thank you. I don't use PME for the long-range electrostatics but the reaction field method.
At least regarding the RMSD of the ligand atoms wrt previous frames, can I do this calculation using the Python API or do I have to call an external code like ptraj?

Greetings, I conduct high through-put MD simulations to equilibrate multiple protein-ligand complexes. However, the required simulation time for equilibration is different for each complex. Is it possible to monitor properties like the protein's and ligand's potential energies, the interaction energ...

OK, this doesn't help really. I do both use the CPU platform and OPENMM_CPU_THREADS=12. Anyway, the reason I do the minimization on the CPU is becasue with CUDA mixed precission I get structures with clashes and when I launch MD I get NaN. Now I changed that and do the minimization on CUDA with doub...

As I state above, I do the minimization on CPU platform, this is also returned by the command line you wrote. I have compiled from source the dev version on both my PC and my laptop. On my laptop the CPU minimization runs on multiple threads but on my PC on just one. The only difference I can notice...

I am on Ubuntu 18.04 64-bit, CUDA-10. For energy minimization I ALWAYS use the CPU.

Greetings, I am writing in this thread rather than creating a new one because I encounter a problem with multithreading. I just did a fresh compilation on my PC using the defaults parameters (attached) but when I try to minimize a system on the CPUs I see that only one core is working. The same happ...

You are right. Damn it! This is exactly what I did at the beginning but I had force.addPerBondParameter('x0') force.addPerBondParameter('y0') force.addPerBondParameter('z0') force.addPerBondParameter("k") force.addGroup(ligatoms) force.addBond([0], [k, x0, y0, z0]) and thus the ligand was drifting.

Greetings, I want to add a CustomCentroidBondForce between the COM of the ligand and it's initial COM coordinates x0,y0,z0. For this purpose I thought to add a dummy atom to the system with mass=0. However, I still can't find how to set it's coordinates to x0,y0,z0. This is how my code looks like: #...

Can I apply this conditional restraint with CustomCentroidBondForce, namely if the distance is greater than the cutoff apply a force, otherwise not?

OK, I did some progress. I pass through the command line the coordinates of the COM of the ligand and set up distance restraints for the waters as follows: # Set up the distance restraints for the waters if args.ligand_COM: force = CustomExternalForce('1000*max(0, r-'+str(0.1*args.WATER_CUTOFF)+')^2...