Date: Wed Nov 24 2010 - 10:00:57 CST
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
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.
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
5046.7639 0.0000 37308.6987 -253595.5428 297.4923 3281688.0904 3281688.0904
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
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