Re: detecting vanishing atoms in zero.fep

From: Brian Radak (
Date: Sun Oct 28 2018 - 10:39:22 CDT

Your question seems entirely dependent on the problem under consideration.

Atoms with a flag of 1 get scaled as a function of alchLambda while those
with a flag of -1 get scaled as a function of 1-alchLambda. If you swap the
groups you just change the sign of the free energy that is computed, so
this is somewhat arbitrary and/or a matter of bookkeeping.


On Sat, Oct 27, 2018, 4:39 PM soroush ziaei <>

> hi all,
> i want to know how can i detect which atom should be -1 in fep file in
> order to obtain correct value for delta<g>?
> or please describe some method to generate topology file for a unique
> structure, such as topology file that exist in tutorial (
> best regards,
> soroush

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