[gmx-users] AMBER nonbond params in GROMACS

[Mark Abraham]

Hi,

Thanks for the attention to detail! :-)

On Tue, Feb 2, 2016 at 6:07 AM Patrick Charchar <
patrick.charchar at rmit.edu.au> wrote:

> 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?
>

The AMBER paper you cite isn't very clear on this point, but its parameter
is called R*, and not Rmin. Both AMBER and CHARMM express such parameters
in force field files as R* = Rmin/2, because that is convenient for
implementing the combination rule Rmin_ij = (Rmin_i + Rmin_j)/2. See e.g.
subscript j to Table 14 of the paper you mentioned. (One doesn't want to do
the division in the inner force loops, but it would have been nice to
implement that optimization after reading the Rmin parameter, rather than
in the value that the user might read or write.) You can see e.g. that the
acpype conversion tool has the same factor of 2 you found you needed
http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype/acpype.py
.

GROMACS implements multiple kinds of combination rules, so has to work in a
more general way, and its dedicated grompp pre-processor helps keep such
implementation details where they belong. :-)

Mark

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
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