Re: High VDW energies during minimization and dynamics

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 13 2006 - 13:24:35 CDT

The box being too small seems particularly likely here. Having an overly
dense PME grid shouldn't cause problems; it just makes things run a
little more slowly.
Peter

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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