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
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