I am using the HOOMD-blue package, and I was advised to use force-shifted Leanard Jones potential, with a tree neighbor list. I do not know which parameters I should write for those charged molecules (hard spheres) "'N, charge'" The system would also have some counterions, and they have an impact on the system.
classhoomd.md.pair.ForceShiftedLJ(nlist, r_cut=None, r_on=0.0, mode='none')
nlist = hoomd.md.nlist.tree(
r_buff=0.4, check_period=1, d_max=None, dist_check=True, name=None)
Thanks in advance!
Dear Elsaid Mohamed,
I suggest you to see links and attached files on topic.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547409/
https://link.springer.com/content/pdf/bbm%3A978-94-009-2484-0%2F1.pdf
https://www.imperial.ac.uk/media/imperial-college/research-centres-and-groups/principles-of-biomolecular-systems/MSc.pdf
https://hal.archives-ouvertes.fr/hal-00514995/document
Best regards
Mohamed-Mourad Lafifi Thanks, those papers are useful, but they do not help me.
I did build the model, and I am struggling to apply electrostatic field to the model.
- Badges
- Science topic
- Similar topics
- Engineering
- Modeling