issue solved... thank you.

Ok, in that case it might be a bug? I tried it out on two different machines, both times resulting in the same error msg: Exception: Parse error in expression "(tabulatedFct(lookup1,lookup2)/r)^2": unknown function: tabulatedFct here the files to reproduce the error: https://byu.box.com/s/7vnrlpd86d...

I have been digging through the documentation, but maybe html syntax is the issue here. When it says "To define a function, include a <Function> tag inside the <CustomNonbondedForce> or <CustomGBForce> tag", I thought it means: <CustomNonbondedForce energy="tabulatedfct(lookup1,lookup2)" bondCutoff=...

Thank you, Peter. I am struggling with addTabulatedFunction inside of the forcefield .html: <CustomNonbondedForce energy="(Bij(lookup1,lookup2)/r)^2" bondCutoff="3"> <PerParticleParameter name="lookup"/> <Atom type="0" lookup="0"/> <Atom type="1" lookup="1"/> <Function name="Bij" type="Discrete2DFun...

Hello,

Very basic question that I could not find an answer to. How can I tell the PDBreporter to only write out the protein coordinates and omit solvent/ions? My trajectories are unnecessarily large as I do not care about solvent positions.

Thank you,
Dennis

Hello, I am looking for an elegant way to encode non-bonded interactions that are dependent on the atom-pair for an ions only simulation. Example: Atomtype A Atomtype B Atomtype C Functional form: V(r) = interaction_AB / r_AB I would need to parametrize a forcefield to contain all the pairwise terms...

Hello, I am adding position restraints via a CustomExternalForce according to methods described here: https://onlinelibrary.wiley.com/doi/full/10.1002/prot.25759 Unfortunately, I seem to run into problems with PBCs as discussed elsewhere on the forum/issue tracker. The error I get suggests a blow up...

Thank you Peter, this was very helpful. We have now CUDA10.0 installed and I get the following performance in agreement with your description: Number GPU 1, ns / day = 158.2310109781112 Number GPU 2, ns / day = 214.0911588615499 Number GPU 3, ns / day = 195.70180466219216 Number GPU 4, ns / day = 17...

Thank you for the speedy reply. Here a lengthy, but hopefully complete description of the situation: python -m simtk.testInstallation: OpenMM Version: 7.4.1 Git Revision: 068f120206160d5151c9af0baf810384bba8d052 There are 4 Platforms available: 1 Reference - Successfully computed forces 2 CPU - Succ...

Hello, I attempted to benchmark OpenMM on a new Cluster with 8 Nvidia Quadro RTX 5000 and CUDA10.2 installed. For a test protein with 120 AA with explicit solvent ~50,000 atoms, I get a performance of ~5ns / day on 4 GPUs. Checking utilization with nvidia-smi shows ~95% usage of GPUs. I found a post...