I have been able to do some testing. First I tried the script I used in the first post and the DNA behavior was still the same. Then I realized that in those tests I was loading the prmtop file and assigning PB radii using parmed, which defeats the whole purpose of the test. It seems that, when I wr...

Nice. I will use those modifications to pdbNames.xml and customgbforces.py on a local openmm enviroment until a new cuda101 ppc64le package is released.

Thank you very much!

Wonderful! If I can help in any way, please let me know.

Sorry for the late reply. I did not test GBn with amber 18, I only tested GBn2 (igb=8). However, when running GBn in the tests I did with openmm (https://drive.google.com/open?id=1rdtb1VYCcWjiVLQ5DSYC9TmJSLf-L1r-), the dsDNA rapidly dissociated into two single stranded DNA molecules, which I don't t...

Thank you very much!

Thank you very much for your help! To be honest, I have no idea who we could ask. The amber reflector (amber@ambermd.org) is publicly available but it specifies that should be used for "scientific questions about installing or using Amber". On the other hand, the corresponding author of the paper us...

I am afraid there might be a problem with the current parameter specification. In amber, nucleic acids have separate parameters of igb=8 (i.e. GBn2). In pages 62 and 63 of amber 2019 reference manual (http://ambermd.org/doc12/Amber19.pdf) the parameters indicated are (I have edited out the alpha, be...

I think I can try to do what you say. Printing forces atom-by-atom seems reasonably trivial in amber (http://archive.ambermd.org/201502/0174.html), and, as far as I know, gb radii are present in plain text in the prmtop file, so I should be able to extract those as well. Regarding OpenMM, it is pret...

Hello all. I am facing the following problem and I don't know if I am missing something really obvious or if it is an actual bug. When simulating dsDNA with implicit solvent models, GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18. Running implicit sol...