Hi everyone,

I wanted to ask if there is support for constant pH simulations in OpenMM and any tutorials for it.
I've found this old repo but have no idea if this was tested and implemented in OpenMM.



Best,
Hassan

Restraining them in position will allow them to keep their shape but will not allow the backbone to relax. So essentially we want the peptides to rotate/translate but not lose the fold.

Hello everyone! I have a polymer with short peptides as repeating units. In the initial minimization, the relaxation of the polymer backbone destroys the fold on some of the peptides. Is there a way to maintain the conformation of the peptides until the relaxation is over, and lift these restraints ...

Hi everyone! I've found the following error in numerous work units in projects that I am running at Folding@Home. The system has angle/distance restraints. Configuring CPU/Reference platform for sanity checks... Using CPU platform for reference calculations. Performing initial sanity checks before s...

So I'm assuming the constraint would have to be implemented by fixing a dihedral somewhere along the polymer backbone? The chain does collapse eventually into a more compact structure but despite that it is longer in the length dimension, and the ultimate objective is to run random mutants therefore...

Hello all, I have a polymer with each repeating unit as a peptide sequence. 15 units in total. I setup the simulation from a stretched out position, I set my box size to +2nm buffer on all sides. But the issue is that if the polymer rotates, it will interact with its periodic image because the heigh...

Got it, thanks!

Yes, the systems are already solvated.

Hello,

I wanted to ask if there is a way to add ions to neutralize the system without using the addSolvent function.


Best,
Hassan

I figured it out, thanks.
My mistake was loading a checkpoint file after setting the masses to zero.

The atoms seem to be moving in the simulation. I used the following code to set the SD atoms mass to zero before creating the Simulation object totalrestrainedatoms=['SD'] for i, atom_crd in enumerate(parm.positions): if parm.atoms[i].name in totalrestrainedatoms: system.setParticleMass(i, 0.0)