[gmx-developers] LJ energy in

[Markus O Kaukonen]

Dear all,

What is the formula for the Lennart-Jones energy (LJ (SR) )
when using gromacs parameters
(
1: Gromacs Forcefield with all hydrogens (proteins only)
ffgmx2nb.itp
)

having entries looking like:

>[ nonbond_params ]
>  ; i    j func          c6           c12
>    O    O    1 0.22617E-02   0.74158E-06
>    O   OA    1 0.22617E-02   0.13807E-05
>    O   OW    1 0.24329E-02   0.18255E-05
> ...

Is the LJ (SR) energy of the form (eqs 4.3 and 4.5 in manual 3.1.1)
A) V_ij = Sum_i_lt_j {c_ij_12/r_ij^12 - c_ij_6/r_ij^6} kJ/mol
or
B) V_ij = Sum_i_lt_j {4*eps_ij*[(sig_ij_12/r_ij)^12 - (sig_ij_6/r_ij)^6]}
kJ/mol
or
C) something else


Best Wishes, Markus

-- 
-----------www= http://www.iki.fi/markus.kaukonen---------------
Markus.Kaukonen at helsinki.fi   \ HOME->   Verajakallionkatu 6 a 5
Helsinki Bioenergetics Group   \_______  02600 Espoo, Finland
Institute of Biotechnology             \ tel:+358-(0)9-5127122/h
Biocenter 3, P.O.BOX 65 (Viikinkaari 1) \____
FIN-00014 University of Helsinki              \______ H+ ______
tel: +358-(0)9-19159752/o, fax: +358-(0)9-19159920             \
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---