From: wenchangyu2006_at_gmail.com
Date: Wed Nov 24 2010 - 10:00:57 CST
Hi all,
I've set up the RBCG model for my system. After 10000 steps minimization
with restraints on backbone, I go equilibration still with
restraints. Right after namd finished startup and going to run, the error
of "Atoms moving too fast" appeared.
I checked the possible reasons according to the page
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting and
also some information online. .pdb and .psf file are looking good and there
is no long bond. Boundary condition is also ok. Then I've no
idea what I still have to check to solve this annoying problem. Could
somebody help me out? Thanks a lot.
Best,
Wenchang
One piece of error massage:
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.50463e-36 AT 30.3305
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 2.74312e-16 AT 29.9322
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 5.04871e-29 AT 29.9322
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.99388e-16 AT 29.9322
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.04871e-29 AT 29.9322
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 3.94091e-16 AT 29.9322
Info: Entering startup phase 8 with 74624 kB of memory in use.
Info: Finished startup with 76304 kB of memory in use.
ERROR: Atom 5152 velocity is 4496.2 2317.22 794.645 (limit is 500)
ERROR: Atom 5153 velocity is -9012.98 -4676.19 -1617.27 (limit is 500)
ERROR: Atom 5155 velocity is 4508.66 2344.64 813.029 (limit is 500)
ERROR: Atoms moving too fast; simulation has become unstable.
ETITLE: TS BOND ANGLE DIHED CROSS IMPRP ELECT VDW
BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 7946.7004 18685.5535 12671.4704 0.0000 0.0000 -13118.0793
-322136.6503
5046.7639 0.0000 37308.6987 -253595.5428 297.4923 3281688.0904 3281688.0904
297.4923
110858.9839 110858.9839 4420898.7671 110858.9839 110858.9839
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Exiting prematurely.
==========================================
WallClock: 15.457838 CPUTime: 15.455651 Memory: 433384 kB
Program finished.
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