[gmx-users] A strange interaction energies...

bmbbl at leeds.ac.uk bmbbl at leeds.ac.uk
Tue Jul 26 15:05:30 CEST 2005

Dear all,

I use "rerun" method to estimate FE difference between the protein and ion.
I perturbated a charge on the ion from 0 to +1.

Certainly, there is no Coulomb interactions between the ion and other atoms in
stateA, where no charge is on the ion.

The strange thing is there is no coulomb interactions, either, including SR and
LR  when the perturbation in .mdp was on to work out the energies in stateB
using the same trj from stateA.

Hereis the ion.itp I use for stateA and stateB
[ moleculetype ]
; molname       nrexcl
K               1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr   charge
;for free energy calculation
; id attype  res nr  residu name  at name  cg nr  charge   mass      attypeB
chargeB massB
  1    K     1          K         K        1      0.00      39.1000    K     
1.00    39.1000

What I have done wrongly?

Thank you.


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