From: Mare Libero (mareliber27_at_yahoo.com)
Date: Wed Mar 26 2014 - 10:12:13 CDT
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?
- 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.
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
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