Re: Stack Traceback problem in colvar restrain

From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Thu Oct 26 2017 - 07:35:09 CDT

Dear Giacomo,
Now my job running well. I have changed the restart frequency to 100. I
have been stuck in this issue from a long time.
Again, thank you so much for your valuable comment.

Best,
Priti

On Wed, Oct 25, 2017 at 10:49 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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