From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Mar 26 2014 - 02:34:20 CDT
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. http://www.avast.com
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:15 CST