[gmx-users] TI with nonbond_params

aherz aherz.kazan at arcor.de
Thu Dec 18 13:54:36 CET 2008


I'm running a TI perturbing the lennard jones parametters of an ion.
In addition I have specified the lj interaction of that ion with water
using nonbond_params like this:

#include "ffG53a6.itp"

[ atomtypes ]
;name   at.num   mass     charge  ptype    c6              c12
 NaMod   CA1      0.000    0.000   A       7.20e-5        2.1025e-08

[ nonbond_params ]
;A      B    1        c6        c12
NaMod  OW   1       -5.116e-7  2.35335e-7

[ moleculetype ]
; Name                     nrexcl
CatC6                      1

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge    mass
typeB    chargeB  massB
    1      NaMod   1     CAT      CA1    1        0.0       22.9898
DUM      0.0      22.9898

#include "spc.itp"

#include "ions.itp"

[ system ]
; Name
Solvated Cation with inverted C6 in water

[ molecules ]
; Compound          #mols
CatC6               1
SOL               893

Will gromacs perturb the nonbond_params or will it only perturb the
parameters specified in atomtypes?
So are the lennard jones params actually going to 0 or are they fixed at
the values specified for nonbond_params no matter what lambda value I use?


More information about the gromacs.org_gmx-users mailing list