Hi,
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?
Thx,
Alex
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