Re: High VDW energies during minimization and dynamics

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Apr 13 2006 - 12:47:30 CDT

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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