Hi,
In the case of windowed aMD (i.e. scaling down barriers), the form of the boost potential is different (see doi: 10.1021/ct200615k).
Therefore, part of the calculation differs, for example the value of EV (EthreshP - totalenergy) is multiplied by -1 (due to windowed aMD applying the boost when the potential energy is above EthreshP).
Additionally, there is extra code to calculate the windowed factor and derivative (see the "(w_amd .ne. 0)" conditional in the previously mentioned sander amd.F90 module).
Best regards,
Irfan Alibay
PhD Student
The University of Manchester, UK
________________________________________
From: Sonia Ziada [sonia.ziada.gmail.com]
Sent: Monday, June 12, 2017 1:53 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
Dear Irfan Alibay,
Thank you very much for your answer. What did you mean by "disregarding the
w_amd mode". Because my goal is precisely to understand the code (amd.F90
module file, subroutine "calculate_amd_total_weights") in the different
cases (mode) and to be sure to interpret the code well (especially the text
in bold):
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 ?*
Thank you. 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
2017-06-12 14:02 GMT+02:00 Irfan Alibay <irfan.alibay.manchester.ac.uk>:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 12 2017 - 07:00:03 PDT
