AW: Question about accelerated MD

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

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