[gmx-users] AMBER nonbond params in GROMACS

[Patrick Charchar]

Hello Gromacs Users,

Sorry if this is trivial, but can someone please explain to me why LJ sigma
values in the gromacs implemented amber FFs (ffnonbonded.itp) are
multiplied by an additional factor of two when converting them from the
values given in the amber papers?

To check my sanity... the van der Waals parameters in amber are given as
R_min (in angstrom) and epsilon (in kcal/mol) - see Cornell, W.D., et al.,
J. Am. Chem. Soc. 117 (19), 5179-5197 (1995).

So to convert to gromacs units:
sigma (in nm) = R_min (in angstrom) / 10 * 2^(-1/6)
epsilon (in kJ/mol) = epsilon (in kcal/mol) * 4.184


Using sp3 carbon as an example, from amber:
R_min = 1.9080 angstrom
epsilon = 0.1094 kcal/mol

After converting I get:
sigma = 0.169983475 nm
epsilon = 0.4577296 kJ/mol

whereas in ffnonbonded.itp:

[ atomtypes ]
; name      at.num  mass     charge ptype  sigma      epsilon
CT           6      12.01    0.0000  A   3.39967e-01  4.57730e-01
Have I missed something?

Thank you for your time.
Regards,

--
Mr. Patrick Charchar
PhD Candidate

School of Aerospace, Mechanical and Manufacturing Engineering
RMIT University
Melbourne Victoria 3001,
Australia

Office phone: +(61 3) 9925 3239
http://www.rmit.edu.au/staff/patrick-charchar