My understanding is that:
if iamd=2, the condition is totdih_ene < EthreshD
if iamd=1 or iamd=3 , the condition is totenergy that equal to (totpotenergy + E_dih_boost) < EthreshD
in witch E_dih_boost is pre-calculated as in iamd=2
the difrence between iamd=1 and iamd=3 is that
in iamd=1, E_boost = E_total_boost
in iamd=3, E_boost = E_total_boost + E_dih_boost (as extra boost) as in DOI: 10.1063/1.2789432
I am not sure.I hope someone confirms or corrects what I have written
I have another question:
what does it mean the "totpotenergy" in the code. The dihedral potential is included in or not?
Hagrouna sadiki
________________________________
From: Sonia Ziada <sonia.ziada.gmail.com>
Sent: Monday, June 12, 2017 4:36 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
Completely agree with you. My goal here was to validate the general
expression of the conditions of application of the boost potential
(deltaV(r)) and the expression of the boost potential in the cases where
iamd=1 or 3 . I did not mention the case of windowed aMD or when w_amd .ne.
0, because the general expressions are the same expect the fact that
E_total_boost
is multiplied by windowed_factor when w_amd .ne. 0 is verified, and
the sign of EthreshP - total energy (versus total energy - EthreshP).
Thank you for all your comments. All other remarks are welcome.
Regards, Sonia.
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Received on Mon Jun 12 2017 - 08:00:03 PDT
