Hello, I'm trying to run the script from here: http://openmm.org/tutorials/alchemical-free-energy/ But got "Particle coordinate is nan" while running. Do you know why? Thanks. Here is my version. and I tested with openCL and CPU, both got the error. openmm 7.4.1 py36_cuda101_rc_1 omnia openmmtools 0...

Can I update the parameter when some condition are met. for example, when two atom are close to each other and their total kinetic energy is larger than certain threshold?
Thanks.

In CustomNonBonded force, we can specify the parameters for each atoms. But If I want to simulate a possible reaction: when two atoms come close enough, they react to each other, how can I change the parameters after the step the reaction happened. It will be great if OpenMM can support this.
Thanks.

I'm using openMM 7.4.1, py36_cuda101_rc_1.

Hello Peter, We encounter a strange bug: the single and double precision gives different energy for our CustomHbondForce force. In the attachment is a much simplified code, so you should be able to reproduce easily. (by doing "python simplified_code.py" to use single precision, and "python simplifie...

great advice. I didn't realize I could using addExclusion() to prevent the self interaction. I will test it out. Thanks!

right. It is a coarse grained force field. Only one term for each pair of residues. The function will be pairwise between the CB of all residues.(but modulated by the CB of residues near them in sequence) the term for each pair will be a function depends on r_ij, r_(i+4,j+4) and some parameters wher...

Thanks for the quick reply. It should be a non-bonded force. and it is a pairwise term at its core, so it will be n^2. but with some additional information required. for example, when compute the interaction between residue i and residue j, I want the energy modulated by the distance between the CB ...

Hello, I want to implement a complex potential for coarse grained simulation. The potential is a pairwise function, but requires the positions of four atoms. There is one interaction between each pair of residues. The force is applied to the CB atom of each residues. the interaction of two CB atoms ...

Hello Peter, I have a similar problem. but a little more complicate. The potential I want to add is not a LJ potential.(it's defined by tabulated continuous function) so I would hope to have a mixed Discrete-Continuous tabulated function. To be more specific, the input array will be 3D. The first 2 ...