From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 25 2017 - 10:55:59 CDT
This looks like there was some I/O error. What version of NAMD are you
using? Try upgrading if it doesn't work.
Also, it is generally *not* a good idea to write DCD files and the Colvars
state file at every step.
Giacomo
On Wed, Oct 25, 2017 at 8:46 AM, PRITI ROY <priitii.roy_at_gmail.com> wrote:
> 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
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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