AMBER Archive (2006)

Subject: AMBER: question on chargning free energy in solvent vs vacuum

From: Lwin, ThuZar (
Date: Thu Aug 03 2006 - 12:08:07 CDT


   I have been learning Tutorial on Dr. Case's thermodynamic

When I calculate charging free energy in Vacuum, in my md print outs
EELEC and 1-4 EEL terms are zero, which to me makes sense since I have
set the charges to zero.


But when I simulate the system in solvent, the EELEC and 1-4 EEL terms
are no longer zero (even though I have set the charges of the atoms on
toluene to zero). While I can understand partly why EELEC is non-zero
(this is due to the charge to charge interactions of water molecules), I
do not know why 1-4 EEL is NOT zero. 1-4EEL is the interaction
separated by 3 bonds and all charges on toluene are zero. I am
wondering where else this 1-4 EEL could have come from. Or could I be
making mistakes in preparing the parm file?



The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to