GROMACS version: 2021.4
GROMACS modification: Yes/No
I downloaded polarizable force field drude-2013f_2018_10.ff from MacKerell Lab to use in GROMACS.
How to calculate sigma and epsilon of pairs in the file drude-2013f_2018_10.ff/ffnonbonded.itp from individual atom’s sigma and epsilon values?
Any help is appreciated.
Thank you.
Best regards,
Nagaraju
The Drude nonbonded scheme uses the same combination rule as the CHARMM force field.
Thank you very much Jalemkul for your response. I could not find the formula to reproduce the nonbonded pair’s sigma and epsilon values. Could you please send an article or formula to calculate the nonbonded pair’s sigma and epsilon values?
Thank you very much.
Have a nice day!
Best regards,
Nagaraju
This documentation page lists the formula that are used for LJ parameters.
Note, that you usually do not have to calculate them on your own. Gromacs does this for you. In forcefield.itp comb-rule is set to 2 which refers to the Lorentz-Berthelot rules.
Hi mbernhardt,
Thank you very much for your reply and information. I used these formulas to calculate pair types in ffnonbonded.itp file in drude force field file from individual sigma and epsilon values, but the values are not reproduced in pair types.
I want to include user-defined atom types in the force field with sigma and epsilon values. I would like to calculate sigma and epsilon for pair type between user-defined atom type and SWM4-NDP water models. For this I need the formula they used for pair type in ffnonbonded.itp file.
Any help is appreciated.
Thank you very much.
Have a great day!
Best regards,
Nagaraju
[pairtypes] and [nonbond_params] that you find in that file are combinations that override combination rule values for specific interactions they will, by definition, not be reproduced by the normal LB combination rule values. All other combinations are generated automatically from the combination rules.
Thank you very much for your information.
Have a great weekend.
Best regards,
Nagaraju