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#37384 - 03/15/19 12:55 PM Units of the parameters in CHARMM36 forecefiled
Mohsen Offline
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Registered: 03/01/19
Posts: 10
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.

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#37386 - 03/15/19 01:50 PM Re: Units of the parameters in CHARMM36 forecefiled [Re: Mohsen]
rmv Offline

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Posts: 8394
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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.
_________________________
Rick Venable
computational chemist


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#37388 - 03/15/19 02:17 PM Re: Units of the parameters in CHARMM36 forecefiled [Re: Mohsen]
Mohsen Offline
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Registered: 03/01/19
Posts: 10
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?

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#37390 - 03/15/19 02:51 PM Re: Units of the parameters in CHARMM36 forecefiled [Re: Mohsen]
rmv Offline

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Registered: 09/17/03
Posts: 8394
Loc: 39 03 48 N, 77 06 54 W
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).
_________________________
Rick Venable
computational chemist


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