From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Jun 29 2011 - 01:25:35 CDT
Have a look at the atoms with the large velocities, this may give you
a hint as to what is going wrong. You might have some badly placed
atoms that the minimizer can't get rid of, or the system is forming
bubbles. You can try running NVT for a few ps before switching to NPT.
Cheers,
Johan
------------------------------------------------------------------------------------------------------
Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Wed, Jun 29, 2011 at 2:06 AM, bharat gupta <bharat.85.monu_at_gmail.com> wrote:
> I did equilibration after minimzation of 20000 steps , I am getting
> following errors during equilibration:-
> REASSIGNING VELOCITIES AT STEP 0 TO 0.5 KELVIN.
> ERROR: Atom 987 velocity is -4.97359e+007 1.4246e+007 -9.72224e+007 (limit
> is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 1240 velocity is 3.36992e+009 6.45705e+009 -7.44682e+009 (limit
> is 12000)
> ERROR: Atom 1242 velocity is 14634 1513.07 -3196.57 (limit is 12000)
> ERROR: Atom 1245 velocity is -127634 -41660.9 39388.9 (limit is 12000)
> ERROR: Atom 1296 velocity is -2.8896e+009 -5.53689e+009 6.38561e+009 (limit
> is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 963 velocity is 4.1778e+006 -1.19928e+006 8.16311e+006 (limit is
> 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
> ENERGY: 0 3504.0840 2149.0188 952.3792 229.8267
> -33464.9911 9999999999.9999 0.0000 0.0000
> 19.6729 9999999999.9999 0.4956 9999999999.9999 9999999999.9999
> 0.4956
> ERROR: Exiting prematurely; see error messages above.
> ====================================================
> WallClock: 0.866000 CPUTime: 0.866000 Memory: 39.414063 MB
> Program finished.
>
> This is my equilibration configuration file:-
> structure ../common/complex_ionized.psf
> coordinates ../common/complex_ionized.pdb # not taken into
> account
> #binCoordinates ../common/complex_eq.coor # this one instead
> extendedSystem ../common/complex_eq.xsc
> outputname equilibrated
> cutoff 12.0
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 8.0
> DCDFreq 1000
> restartFreq 1000
> parameters ../common/par_all27_prot_na.prm
> paraTypeCharmm on
> berendsenPressure on
> berendsenPressureTarget 1.01325 # atmospheric pressure
> berendsenPressureCompressibility 4.57e-5 # liquid water
> berendsenPressureRelaxationTime 100.0
> berendsenPressureFreq 10
> temperature 0.5 # starting at 0.5 K
> reassignFreq 100
> reassignIncr 0.5
> reassignHold 300 # target T: 300 K
> numsteps 100000 # 100 ps, constant T the last 40 ps
>
> Can anybody tell be how to rectify the errors for those atoms.
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010_at_yahoo.com
>
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