From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Fri Feb 27 2015 - 18:15:13 CST
Google seems to bring up various threads involving potential bugs with
accelerated MD and GBIS. However I seem to be seeing similar problems in a
slightly different context.
I am running implicit solvent aMD with a dipeptide on NAMD multicore (*not*
CUDA). In normal dihedral only mode, the dihedral energy in the aMD and
ENERGY fields never seem to differ, even when dV comes back non-zero. Here
is my first frame:
ACCELERATED MD: STEP 0 dV 1.10188 dVAVG 1.10188 BOND 4.04848 ANGLE 12.6857
DIHED 16.3605 IMPRP 0.371159 ELECT -155.46 VDW -1.45463 POTENTIAL -123.449
ETITLE: TS BOND ANGLE DIHED
IMPRP
ELECT VDW BOUNDARY MISC
KINETIC
TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG
ENERGY: 0 4.0485 12.6857 16.3605
0.3712
-155.4598 -1.4546 0.0000
0.0000 20.6767
-102.7719 320.1538 -123.4486 -102.5823
320.1538
Here accelMDE = 18.0 and accelMDalpha = 0.8. I'm a little new to aMD, so I
can't tell if this is a particularly aggressive boost or not (based on the
NAMD aMD paper and alanine dipeptide, it should be pretty good). However,
my phi/psi coverage seems to be pretty poor after 5,000,000 steps.
Is something wrong here or am I misunderstanding the output and/or using
poor boost parameters?
Thanks,
Brian
-- Brian Radak Postdoctoral Scholar University of Chicago Department of Biochemistry & Molecular Biology Gordon Center for Integrative Science, W323A 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 e-mail: radak_at_uchicago.edu
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