From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Wed Oct 25 2017 - 12:11:52 CDT
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
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
>
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