From: Ryan McGreevy (ryanmcgreevy_at_gmail.com)
Date: Wed Mar 26 2014 - 11:19:17 CDT
The ELECT, VDW, and POTENTIAL terms could be different if you are using a
CUDA version of NAMD and implicit solvent, due to a bug. If this is the
case, it has been fixed and is currently available in the nightly NAMD
builds.
On Wed, Mar 26, 2014 at 10:36 AM, Thomas Evangelidis <tevang3_at_gmail.com>wrote:
> 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