[gmx-users] question regarding free energy calculations

[Asaf Farhi]

Dear all

Hi. We have a question regarding the implementation of free energy calculations in Gromacs that we have been trying for long time to decipher.

The question is the following:

When transforming molecule A to B if the non bonded interactions are changed through the topology file e.g:
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass   typeB  chargeB  massB
    1    HC    1     PCH3    H1    1    0.123   1.0080   HC    0.0      1.0080

, will the the interactions of this atom with all the other atoms be affected by this change of charge?

We will really appreciate help.

Thanks in advance,
Best regards,
Asaf