Virtual sites for DNA

User discussions
1

GROMACS version: 2020
GROMACS modification: /No

Dear all,
I am writing to you because I would like to implement virtual sites in MD simulations of nucleic acids for two different all-atom force fields (AMBER14 with parmbsc1 corrections and the march 2019 version of CHARMM36m). Unluckily, I could not find any reference in literature for simulations of NA with virtual sites (not even limited to the treatment of hydrogen atoms). Do you know of any results on the matter? And also, what artefacts did you observe in the treatment of aromatic rings (section 5.8.10 of 2019 manual) in peptide residues?

Thank you for your time,

Vincenzo

2

Dear Vincenzo,
Sorry for the late reply. We have made this tool MkVsites (https://github.com/ErikMarklund/mkvsites). We are about to start an investigation about how the vsite parameters work with nucleic acids, because as far as I know there have not been any systematic evaluation of DNA. Give me a shout if you need help with using the tool. It can be a bit tricky sometimes.
Kind regards,
Erik