Hi,
Instead of: if iamd=1 or iamd=3 , the condition is totenergy that equal to
(totpotenergy + E_dih_boost) <* EthreshD*
It is : if iamd=1 or iamd=3 , the condition is totenergy that equal to
(totpotenergy + E_dih_boost) <* EthreshP*
For the rest, if you consider the same expression of E_dih_boost and
E_total_boost
as me. I agree with you.
Concerning your question, from my personal understanding, the dihedral
potential is included in totpotenergy. Other opinions for this relevant
question ?
Sonia Ziada.
*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
2017-06-12 16:42 GMT+02:00 Hagrouna sadiki <hagrouna.sadiki.outlook.com>:
> 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 - 08:30:02 PDT
