Dear Amber users:
After experimenting a little with Belly using Ewald, I found something
I didn't expect about the MD output energies. Could anybody please
check that what I understand is correct?
In the standard output there are, among several other quantities, one
called EELEC and another called 1-4EEL. The 1st one gives the total
Ewald electrostatic energy of the system, with the exception of the
1-2, 1-3 and 1-4 interactions (or are those terms also included?). The
2nd one gives a 1-4 electrostatic energy, calculated outside Ewald, I
imagine in the same way that the others (BOND, ANGLE, etc.) are
calculated. So that if you put together EELEC + 1-4EEL, you get the
total electrostatic energy of the whole system (of course, except 1-2
and 1-3 interactions).
So far, so good. But I found out that if you use belly, then the
1-4EEL (along with BOND, ANGLE, etc.) ignore the energies between
fixed atoms. On the other hand, the Ewald calculation, and thus EELEC,
is unaffected by belly, so that energy does include even the fixed
atoms. So EELEC and 1-4EEL are incompatible! Consequently, if we do
EELEC + 1-4EEL, we don't get the total electrostatic energy of the
system.
This could not be a problem, depending on what you are calculating. In
particular, if you do charge TI, DV/DL is obtained from (EELEC +
1-4EEL), so you may have big problems here...
If anybody has some comment on this I would really appreciate it.
Ignacio
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Received on Thu Jul 28 2011 - 13:00:07 PDT
