[gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Daniel Bauer]

Hello,

I finally found my error in the conversion. As always, the devil is in
the detail. I was under the assumption that parameters listed in the
original forcefield files (toppar) are also sigma and epsilon values.
However, as you know, the original files list Rmin values (and not sigma).

With the correct conversion term:

eps = Rmin/(10*2^(1/6))

I can now reproduce the conversion of the numbers from the charmm
implementation to gromacs (and thus know how to apply my NBFIX for this
value).

Thanks for your patience and best regards,

Daniel


On 12/03/2017 10:18 PM, Daniel Bauer wrote:
> Hello,
>
>
> I compared the LJ parameters for the interaction Potassium - backbone
> carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the
> forcefield. I found different numbers for the sigma value i cannot
> explain to myself:
>
>
> The stock charmm36 implementation has the following LJ parameters for
> potassium and oxygen:
>
> ; atom    Emin (kcal/mol)    Rmin/2 (A)
>
> POT    0.087    1.76375
>
> O    0.120    1.7
>
>
> Converting the above values to units used in gromacs (kJ/mol and nm) and
> applying standard combination rules this should give the following
> nonbonded energy parameters:
>
> [ pairtypes]
>
> ; sig = (Rmin,i/2 + Rmin,j/2)/10
>
> ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ
>
> ; i    j    func    sig (nm)    eps (kj/mol)
>
> O    POT    1    0.346 0.4275
>
> However, the actual entry for the interaction in GROMACS/charmm36 has
> the energy minimum at a much smaller distance (epsilon is on the point
> though!)
>
> ; i    j         func     sig (nm)        eps (kJ/mol)
>
> O    POT    1    0.282    0.4275
>
>
> Can somebody tell me the reason for this huge difference? Is there an
> error in my calculation? I am trying to convert an NBFIX applied to this
> specific interaction to gromacs. However, I am not sure how to proceed
> without doing the reparametrization in gromacs again, because the stock
> values differ that much.
>
> Best regards,
>
> Daniel
>
>

-- 
Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
bauer at cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.