From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Mon Mar 31 2014 - 03:57:30 CDT
I was going through some accelerated MD runs that I am performing and i
realized that in the log file the van der Waals energy does not coincide
in the ENERGY and ACCELERATED parts.
ACCELERATED MD: STEP 84060000 dV 38.9411 dVAVG 44.0163 BOND 931.749
ANGLE 2196.73 DIHED 4204.91 IMPRP 0 ELECT -374706 VDW 43781.7 POTENTIAL
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 84060000 931.7490 2196.7340 4204.9080
0.0000 -374705.9991 42347.8873 0.0000 0.0000
56808.4961 -268216.2248 299.6215 -325024.7208
-268132.5131 298.0088 106.7328 105.3388
942343.9347 -0.6257 -0.6533
I think the issue is that i am using the LJ correction for the long
range interactions and that is not being considered in the dV calculation.
For my case it is not a problem since i am using only dihedral acceleration.
Also, on a related topic, does somebody know any tool to re-weight the
sampling after aMD? I am having some issues with the tools i created
mainly because there are some frames with quite high biasing which don't
do any good to my final histograms, and i'd like to compare with another
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