Re: Stack Traceback problem in colvar restrain

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 25 2017 - 12:19:16 CDT

Check the value of restartFreq below:

On Wed, Oct 25, 2017 at 1:11 PM, PRITI ROY <priitii.roy_at_gmail.com> wrote:

> Dear Giacomo,
> AT first thank you for your suggestion. The NAMD version I'm using is 2.12
> which is the recent version. I also simulated same protein without restrain
> with same NAMD version. That time there was no problem.
> My input file is as follows:
> =========================================================================
> coordinates ../../ionized.pdb
> structure ../../ionized.psf
> paraTypeCharmm on #parameter file is charmm type
> parameters ../../par_all22_prot.prm
> bincoordinates ../../min01.coor
> extendedSystem ../../min01.xsc
> binvelocities ../../min01.vel
>
> outputname npt01 #writes final .vel and .coor
>

This line will make NAMD write files at every step: please fix it.

*restartfreq 1 #at this frequency *

>
> DCDfile npt01.dcd #writes .dcd file
> DCDfreq 500 #at this frequency
> outputEnergies 2000 #writes energy at this frequency
>
> timestep 2.0 #timesteps are in femtoseconds
> numsteps 500000
> firsttimestep 0 #value of the first time step
> stepspercycle 20 #atoms are reassigned every cycle
>
> cutoff 12.5 #coulomb and vdW in Angs
> switching on #smoothing function for coulomb and vdW
> switchdist 10.5 #distance at which smooth starts (in Angs)
> pairlistdist 13.5 #goes with cutoff
> exclude scaled1-4 #which pair is excluded from non-bonded
> inter
> 1-4scaling 1.0
> rigidBonds all #bonds involving hydrogens are constrained
> fullElectFrequency 2 #time steps between Coulomb evaluation
> nonbondedFreq 1 #time steps between non-bonded evaluation
>
> PME on #use particle mesh Ewald for Coulomb
> PMEGridspacing 1.0
>
> cellBasisVector1 117.17 0.0 0.0 #periodic boundary
> cellBasisVector2 0.0 75.125 0.0 #conditions
> cellBasisVector3 0.0 0.0 88.33
> cellOrigin 1.22 0.049 -2.75
>
> langevin on
> langevinDamping 1
> langevinTemp 310
>
> useGroupPressure yes #must be used with rigigBonds (shake)
> useConstantRatio no #x and y are forced to the same length
> LangevinPiston on #use Langevin piston pressure control
> LangevinPistonTarget 1.0 #pressure in bar
> LangevinPistonPeriod 200
> LangevinPistonDecay 500
> LangevinPistonTemp 310
>
> colvars on
> colvarsConfig colvar.conf
> colvarsInput ../../min01.colvars.state
> ============================================================
> ==================================================================
> As in the input file, there is no option to write colvar.state file though
> it is written in every step. Is any problem in my input file?
>
> Thanks,
> Priti
>
> On Wed, Oct 25, 2017 at 9:25 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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
>>
>
>

-- 
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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