From: Deva Priyakumar (deva_at_outerbanks.umaryland.edu)
Date: Thu Apr 13 2006 - 14:41:22 CDT
Thank you, I increased the cell dimensions and it works fine.
Deva
On Thu, 2006-04-13 at 10:47 -0700, Brian Bennion wrote:
> Hello,
>
> Your box is somehow cutting off a bonded interaction or overlapping
> nonbonding interactions. Looking at the input file, your pme boundaries
> are almost twice the size of your cell.
>
> Checks to make:
>
> Turn off PME and run minimization with PBC on
> Turn on PME and correct your PME cutoffs.
> Double check the VMD output of the measure minmax and measure center
> commands.
>
> Regards
> Brian
>
> On Thu, 13 Apr 2006, Deva Priyakumar wrote:
>
> > Hello,
> >
> > I am a new user of NAMD. will somebody help me with this please.
> >
> > My script looks something like this and the output follows. The VDW
> > energies are meaningless and I do not know where I am going wrong.
> >
> > I checked the coordinates - they are fine.
> > The cell dimensions - i have checked and they are fine
> >
> > when i turn of the periodic boundary conditions the calculation runs
> > fine.
> >
> > Thanks
> > Deva
> >
> > ******************************************************************
> > # molecular system
> > coordinates erk_wat.pdb
> > structure erk_wat.psf
> >
> > # force field
> > paratypecharmm on
> > parameters /raid/deva/parameters/par_all27_prot_na.prm
> > exclude scaled1-4
> > 1-4scaling 1.0
> >
> > # for periodic boundary conditions
> > # replace with your own box dimensions!
> > cellBasisVector1 47.7220001221 0.0 0.0
> > cellBasisVector2 0.0 34.2980003357 0.0
> > cellBasisVector3 0.0 0.0 32.171500206
> > cellOrigin -3.48490834236 -0.0266390871257 0.724303662777
> > wrapAll on
> >
> > # you may use some other numbers.
> > PME on
> > PMEGridSizeX 100 # grid-pts along cellBasisVector1.
> > PMEGridSizeY 75 # along cellBasisVector2.
> > PMEGridSizeZ 75 # along cellBasisVector3
> > ## use numbers with small integer factors: 2,3,5.
> >
> > # approximations
> > switching on
> > switchdist 10
> > cutoff 12
> > pairlistdist 13.5
> >
> > # center-of-mass motion is automatically removed.
> >
> > # integrator
> > timestep 1.0 # in fs.
> > stepspercycle 20
> > nonbondedFreq 2
> >
> > # output
> > outputenergies 10
> > outputtiming 100
> > binaryoutput no
> >
> > outputname test
> > dcdfreq 100 # how often we output trajectories.
> >
> > # for restarting:
> > restartname ilb-min-restart
> > restartfreq 500
> > restartsave yes
> > binaryrestart yes # preserves more accuracy.
> >
> > # no T or P coupling needed for EM.
> > temperature 0 # initial temperature
> >
> > minimize 200 ; # steps to minimize
> > *************************************************************************
> >
> > and the output:
> >
> > Info: Entering startup phase 7 with 46866 kB of memory in use.
> > Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> > Info: NONBONDED TABLE SIZE: 769 POINTS
> > Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.70577e-22 AT 11.9974
> > Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 6.62384e-17 AT 11.9974
> > Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 9.09495e-13 AT 0.03125
> > Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 4.21309e-16 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 2.91168e-22 AT 11.9974
> > Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 6.16001e-17 AT 11.9974
> > Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.98523e-22 AT 11.9974
> > Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 8.0593e-16 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 2.75 AT 0.0441942
> > Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 6656 AT 0.0441942
> > Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.055e-15 AT 0.0441942
> > Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 7.45058e-09 AT
> > 0.0441942
> > Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 7.62939e-06 AT 0.0441942
> > Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
> > Info: Entering startup phase 8 with 50713 kB of memory in use.
> > Info: Finished startup with 53018 kB of memory in use.
> >
> > TCL: Minimizing for 200 steps ETITLE: TS BOND
> > ANGLE DIHED IMPRP ELECT VDW
> > BOUNDARY MISC KINETIC TOTAL TEMP
> > TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE
> > VOLUME PRESSAVG GPRESSAVG
> > ENERGY: 0 10767.9627 12200.0122 1876.4167
> > 2.2438 -105788.7202 -99999999.9999 0.0000 0.0000
> > 0.0000 -99999999.9999 0.0000 -99999999.9999 -99999999.9999
> > 0.0000 -99999999.9999 -99999999.9999 52657.3199 -99999999.9999
> > -99999999.9999
> >
> >
>
> ************************************************
> Brian Bennion, Ph.D.
> Biosciences Directorate
> Lawrence Livermore National Laboratory
> P.O. Box 808, L-448 bennion1_at_llnl.gov
> 7000 East Avenue phone: (925) 422-5722
> Livermore, CA 94550 fax: (925) 424-5513
> ************************************************
>
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