[AMBER] Fwd: Accelerated MD when iamd=1 or 3

From: Sonia Ziada <sonia.ziada.gmail.com>
Date: Mon, 12 Jun 2017 13:45:41 +0200

Dear Amber users,



Concerning accelerated MD, I am not sure I get the point about the
conditions that must be verified to add the boost potential (deltaV(r)) and
the expression of the boost potential in the case where iamd=1 or 3.



Can you please tell me if the following is correct:



E_dih_boost = E_total_boost = E_boost = 0



If ( totdih_ene < EthreshD )

            E_dih_boost = (EthreshD - totdih_ene )2 / (alphaD + EthreshD -
totdih_ene) # expression of the boost potential when iamd=2



If ( iamd==1 or iamd==3 )

If ( tot_potenergy *+ E_dih_boost* < EthreshP ) * # correct ?*

totalenergy = tot_potenergy + *E_dih_boost*

E_total_boost = (EthreshP - totalenergy)2 / (alphaP + EthreshP -
totalenergy ) *# expression of the boost potential when iamd=1 ?*



If (iamd==3)

E_boost = E_total_boost + E_dih_boost *# expression of the boost potential
when iamd=3** ?*



Thanks in advance.


Best regards,

*ZIADA Sonia*
PhD Student, Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
d'Orléans 7311
Rue de Chartres, 45067 Orléans, France
T. +33 238 419 939
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Received on Mon Jun 12 2017 - 05:00:04 PDT
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