From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Wed Oct 25 2017 - 07:46:57 CDT
Dear all,
I have run a simulation with dihedral restrain in some portion of the
protein using colvar module. The minimization step was finished smoothly
but in NPT simulation, after three step the job has been stopped without
mentioning any error. The last portion of output file is as follows:
=======================================================
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 301.1992 994.9985 1227.6809
35.9353 -325284.1312 34048.8108 0.0000
12.4570 0.0000 -288663.0495 0.0000 -288663.0495
-288661.1864 0.0000 -4283.1428 -4250.3788
777515.6608 -4283.1428 -4250.3788
colvars: Synchronizing (emptying the buffer of) trajectory file
"npt01.colvars.traj".
colvars: Writing the state file "npt01.restart.colvars.state".
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1
WRITING COORDINATES TO RESTART FILE AT STEP 1
FINISHED WRITING RESTART COORDINATES
The last position output (seq=1) takes 0.002 seconds, 97.500 MB of memory
in use
WRITING VELOCITIES TO RESTART FILE AT STEP 1
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=1) takes 0.003 seconds, 97.500 MB of memory
in use
colvars: Synchronizing (emptying the buffer of) trajectory file
"npt01.colvars.traj".
colvars: Writing the state file "npt01.restart.colvars.state".
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2
WRITING COORDINATES TO RESTART FILE AT STEP 2
FINISHED WRITING RESTART COORDINATES
The last position output (seq=2) takes 0.001 seconds, 97.500 MB of memory
in use
WRITING VELOCITIES TO RESTART FILE AT STEP 2
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=2) takes 0.001 seconds, 97.500 MB of memory
in use
colvars: Synchronizing (emptying the buffer of) trajectory file
"npt01.colvars.traj".
colvars: Writing the state file "npt01.restart.colvars.state".
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 3
WRITING COORDINATES TO RESTART FILE AT STEP 3
[13] Stack Traceback:
[13:0] [0xf88fa7]
[13:1] [0xb03146]
[13:2] [0x108534e]
[13:3] [0x11a8ee7]
[13:4] [0x132ae15]
[13:5] [0x51b9aa]
[13:6] [0x50f832]
[13:7] __libc_start_main+0xfd [0x3f8e81ecdd]
[13:8] _ZNSt8ios_base4InitD1Ev+0x41 [0x40e469]
=======================================================================
I could not understand this Stack Traceback problem. Before posting this, I
have gone through previous threads related to this issue but none of those
were find useful.
So, kindly give your insights to resolve my problem.
Thanks,
Priti
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