Hi,
>From what I can tell, disregarding the w_amd mode, you are correct.
The code for this can be seen in the sander amd.F90 module file, subroutine "calculate_amd_total_weights".
Best regards,
Irfan Alibay
PhD Student
The University of Manchester, UK
________________________________________
From: Sonia Ziada [sonia.ziada.gmail.com]
Sent: Monday, June 12, 2017 12:45 PM
To: AMBER Mailing List
Subject: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
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 - 05:30:03 PDT
