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

Daniel Bauer bauer at cbs.tu-darmstadt.de
Sun Dec 3 22:26:02 CET 2017


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

; 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 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.

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