I've determined the (proximal) cause to be blowing up of the simulation (the coordinates eventually go wild spontaneously whether I do NPT, NVT, or NPT heating). I don't know what causes it. I am starting from a minimized structure. I tried to attach the pdb and script but it wouldn't let me. Is the...

It crashes every time (this is the third or fourth time today). It's a heating / annealing step. It crashes at 170 K for some reason. I think it crashes at different times for different runs. Could it be an AMOEBA implementation bug?

It says GPU util is 98-100% and the memory usage is only 343MiB / 8192MiB. The cpu memory usage from top is 0.3% (negligible). It runs for 1000s or even 10000s of steps before suddenly crashing. It's definitely integrating I made sure of that. Do you have any idea what could be causing the problem i...

Hi OpenMM, I am trying to run an AMOEBA simulation of a rather large system (81,000 atoms or so). I minimized and equilibrated the solvent just fine, then did more minimizations and that was fine too. But during the temperature annealing / heating step it first of all runs WAY too long for the amoun...

thanks!

Hi OpenMM, I am building an MD engine for a specific project that is difficult to do with standard MD software. I was wondering two things: 1. in the xml files of OpenMM force fields, what are the units of epsilon and sigma in the vdw sections? 2. for vdw interactions, how do you combine the sigmas ...

Yeah, reviewers wouldn't like that hahahahahahaha. I'll try NME.

NME vs NHE shouldn't be a huge deal in terms of my results (nonlinear spectra), although my experimental collaborators use NHE so it would be optimal to be consistent. For now, I took the parameters from the two amide hydrogens of ASN for the NHE hydrogens and NME's nitrogen for the NHE nitrogen bas...

Ok I will try that. In general, would you recommend doing this or just using the NME cap instead? It seems hacky...What do you think?

Hi OpenMM, I have a protein with an amide (NH2) capping group that I want to simulate with AMOEBA. Unfortunately, the OpenMM AMOEBA xml lacks an NHE entry. I added one like this: <Residue name="NHE"> <Atom name="N" type="7"/> <Atom name="HN1" type="152"/> <Atom name="HN2" type="152"/> <Bond from="0"...