From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Dec 26 2016 - 10:49:38 CST
Hmm… What happens if you ask for run 0? That will do an energy evaluation, and should, if I remember correctly, also write the colvars.traj just for that frame. Again, the only thing I can think of is that the distance along the x axis is so small that distanceZ is hitting the lower boundary potential and causing a mess. Others might have better ideas.
Josh Vermaas
Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>
On Dec 26, 2016, at 8:17 AM, Peter Mawanga <peter.mawanga.lagos_at_gmail.com<mailto:peter.mawanga.lagos_at_gmail.com>> wrote:
colvars.traj output:
# step polymerbeadseparation
0 3.00000000000000e+01
10000 2.91237590280440e+01
20000 3.00346690073403e+01
30000 2.82243021688464e+01
I couldn't figure out why is this occurring, given both have the same input files and are running on NAMD 2.12.
Thanks
[https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif]Peter
On Tue, Dec 27, 2016 at 2:07 AM, Peter Mawanga <peter.mawanga.lagos_at_gmail.com<mailto:peter.mawanga.lagos_at_gmail.com>> wrote:
Hello Joshua
The load balancing doesn't start for distanceZ case, hence I am not getting any colvars.traj output either. This is the error:
PRESSURE: 0 -2045.01 -9.4077 22.7297 -9.4077 -29.1219 -2.91884 22.7297 -2.91884 1.2482
GPRESSURE: 0 -2045.01 -9.4077 22.7297 -9.4077 -29.1219 -2.91884 22.7297 -2.91884 1.2482
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 7.0528 11.4618 0.0000 0.0000 -75.4197 -155137.7401 0.0000 0.0000 23072.9575 -132121.6877 309.2266 -155194.6452 -131515.7116 309.2266 -690.9601 -690.9601 3468098.5652 -690.9601 -690.9601
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Atom 2684 velocity is -312318 -220584 242621 (limit is 1200, atom 11 of 43 on patch 345 pe 8)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 345 pe 8).
ERROR: Atom 51 velocity is 311893 220572 -242609 (limit is 1200, atom 7 of 43 on patch 355 pe 8)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 355 pe 8).
ERROR: Exiting prematurely; see error messages above.
Whereas for the case of distance colvar:
PRESSURE: 0 -12.0398 -9.41329 22.7792 -9.41329 -29.1219 -2.91884 22.7792 -2.91884 1.2482
GPRESSURE: 0 -12.0398 -9.41329 22.7792 -9.41329 -29.1219 -2.91884 22.7792 -2.91884 1.2482
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 7.0528 11.4618 0.0000 0.0000 -75.4197 -155137.7401 0.0000 0.0000 23072.9575 -132121.6877 309.2266 -155194.6452 -132107.7606 309.2266 -13.3045 -13.3045 3468098.5652 -13.3045 -13.3045
OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 3.92203
LDB: ============== END OF LOAD BALANCING =============== 3.92287
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 3.96309
LDB: ============= START OF LOAD BALANCING ============== 5.12916
LDB: Largest compute 547 load 0.001950 is 0.2% of average load 0.822949
LDB: Average compute 0.000365 is 0.0% of average load 0.822949
LDB: Partitioning computes with target load 0.082295
LDB: Increased migratable compute count from 11400 to 11400
LDB: Largest unpartitionable compute is 0.001106
LDB: ============== END OF LOAD BALANCING =============== 5.1428
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