From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Mar 26 2014 - 10:36:51 CDT
Στις 26 Μαρ 2014 5:16 ΜΜ, ο χρήστης "Mare Libero" <mareliber27_at_yahoo.com>
έγραψε:
>
> Hi Norman,
>
> Thank you for the reply. I haven't explained myself properly. I am not
sure I completely understand the energy terms reported in the aMD output.
>
> In aMD the potential and dihedral energies are corrected by a boost
potential when the energy crosses a threshold E: V*=V+deltaV where
deltaV=E-V)^2/(alpha+E-V) and alpha is the acceleration.
>
> - In the ENERGY lines: are the energies reported before or after the
correction? (V* or V?).
> - I assume the dV is the deltaV. Is this dV for the total energy or for
the dihedral? What is the difference between dV and dVAVE?
Have searched exhaustively in the mailing list for these terms? I think
your questions have been answered in the past.
> - Also, I am noticing right now that the ELECT, VDW and POTENTIAL terms
in the aMD output line are quite different from the ENERGY output line. I
am not sure what these terms indicate.
Do you use the cuda namd code? What version?
> I guess if I could get more details about the meaning of these reported
energies, that would help me understand how the energy landscape is being
modified; and at which stages of the dynamics the boost potential is
applied or not applied.
>
> Thanks again for the reply,
>
> Alex
>
>
> On Wednesday, March 26, 2014 3:34 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Hi Mare,
>
> well I don’t know much about aMD and that one can turn it on and off
during simulation, but I guess you won’t see lines like:
>
> ACCELERATED MD: STEP 20090000 dV 106.786 dVAVG 119.229 BOND 1778.28 ANGLE
4710.7 DIHED 4280.65 IMPRP 304.643 ELECT -39778.9 VDW -5911.43 POTENTIAL
-34616.
>
> if it is turned off. And you will see such lines if it is turned on. So?
>
> Norman Geist.
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
Auftrag von Mare Libero
> Gesendet: Dienstag, 25. März 2014 23:14
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Question about accelerated MD
>
> Hello,
>
> I have question about accelerated MD. Is there anyway to see from the
output file when the aMD component is turned one and off? I am running aMD
in "dual" mode with and NPT system in explicit solvent.
>
> My average total and dihedral energies as calculate from preliminary
conventional MD are:
> ave Edihe = 2,517.1
> ave Edihe = -218,994.7
>
> And the aMD parameters:
> accelMDE 4549
> accelMDalpha 406
> accelMDTE -205466
> accelMDTalpha 13528
>
> This is how my output looks like:
> ACCELERATED MD: STEP 20090000 dV 106.786 dVAVG 119.229 BOND 1778.28 ANGLE
4710.7 DIHED 4280.65 IMPRP 304.643 ELECT -39778.9 VDW -5911.43 POTENTIAL
-34616.1
>
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL
TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 20090000 1778.2756 4710.7004 4280.6514 304.6426 -305465.4314
24839.6723 0.0000 0.0000 53507.4691 -216044.0201 310.5189 -269551.4891
-215872.3828 309.8437 -44.6743 16.3590 837465.3377 -2.7721 -2.8359
>
> Thanks in advance for any useful comments,
>
> Alex
>
>
> ________________________________
> Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus
Schutz ist aktiv.
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:15 CST