From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Fri Jan 25 2019 - 07:32:43 CST
Dear all,
We are doing some testing using the gaussian accelerated MD implemented
in NAMD. When running with iE=2 (setting the threshold potential at its
maximum value), as soon as the simulation switched from the classical MD
equilibration to gaussian accelerated MD (step 5000000 in this
particular case), I get the warning below. The warning says that k0 > 1
and that is why the simulation switches automatically to iE=1. However,
according to the output k0 is 0.43 for the boost on the dihedral energy
and 0.05 for the boost on the total potential (see below). These are
both below 1 ....
I'd appreciate a lot if somebody could explain whether this is a bug or
am I overlooking something.
Thanks a lot
Best wishes
Vlad
----sample output -----
ACCELERATED MD: STEP 5000000 dV 34.5194 dVAVG 0.0138077 BOND 1320.89
ANGLE 3054.73 DIHED 4612.83 IMPRP 0 ELECT -1.15509e+06 VDW 172575
POTENTIAL -973530 LJcorr -3898.48
GAUSSIAN ACCELERATED MD: DIHED iE 1 Vmax 4740.73 Vmin 4477.74 Vavg
4602.2 sigmaV 26.2707 E 4740.73 k0 0.433587 k 0.0016487
GAUSSIAN ACCELERATED MD: DIHED !!! WARNING: k0 > 1, SWITCHED TO iE = 1
MODE !!!
GAUSSIAN ACCELERATED MD: TOTAL iE 1 Vmax -975387 Vmin -984730 Vavg
-977593 sigmaV 490.889 E -975387 k0 0.0517528 k 5.53917e-06
GAUSSIAN ACCELERATED MD: TOTAL !!! WARNING: k0 > 1, SWITCHED TO iE = 1
MODE !!!
-- Vlad Cojocaru, PD (Habil.), Ph.D. ----------------------------------------------- Project Group Leader Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany ----------------------------------------------- Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de http://www.mpi-muenster.mpg.de/43241/cojocaru
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