[AMBER] Energy shifted energy term

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Thu, 9 May 2019 20:48:42 +0000

Hi Daniel,

There is a energy shifted term in "SPAM" on page 690 of Amber18 manual--->
"Perform profiling of bound water molecules via SPAM analysis[615]. Briefly, this method identifies and estimates the free energy profiles of bound waters via calculation of the distribution of interaction energies between the water and itís environment from explicit solvent MD trajectories. The interaction energies are calculated using a force and energy-shifted electrostatic term with a hard cutoff"

I would be happy to know what is this force and energy shifted electrostatic term?
I would love to get an idea or at least a reference from where this shifted energy term comes from? The SPAM paper says nothing at all!
Also, in LIE page 666 there is a line "The electrostatic interactions are calculated according to a simple shifting function shown below...." Where does that equation come from?
Any reference on that would definitely help.

University of Michigan, USA

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Received on Thu May 09 2019 - 14:00:02 PDT
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