Units of the parameters in CHARMM36 forecefiled

Posted by: Mohsen

Units of the parameters in CHARMM36 forecefiled - 03/15/19 12:55 PM

Dear all,

Hi!

Where can I find units of the parameters in the CHARMM36? For instance, what are the units of the sigma and epsilon in the ffnonbonded.itp file.

Thank you
Mohsen.
Posted by: rmv

Re: Units of the parameters in CHARMM36 forecefiled - 03/15/19 01:50 PM

Most of the units are in the "usage" doc file on the charmm.org web site. Energies are typically in kcal/mol, and distances are in ┼nstroms.

The actual CHARMM force field parameter files have names such as par_all36_prot.prm, so it seems you are using a derived file in some other package. The distributed files tabulate Rmin/2 instead of sigma for the nonbond terms.
Posted by: Mohsen

Re: Units of the parameters in CHARMM36 forecefiled - 03/15/19 02:17 PM

Thanks for your kind answer

I have downloaded CHARMM36 from this webpage:

charmm36-nov2018.ff.tgz in

http://mackerell.umaryland.edu/charmm_ff.shtml

So do you mean that this force field is a derived file?
So finally what are the units of the parameters of sigma and epsilon? Also, do you think that tabulating Rmin/2 instead of sigma is a correct model?
Posted by: rmv

Re: Units of the parameters in CHARMM36 forecefiled - 03/15/19 02:51 PM

That is a conversion of the distributed CHARMM files into GROMACS format, so presumably the change of units and computing sigma from Rmin/2 has already been performed. The units should conform to those used by GROMACS.

Sigma and Rmin/2 can be readily interconverted, but early CHARMM developers chose Rmin/2 to facilitate computing the atom pair values from the simple sum of the self terms (arithmetic combining rule).