Re: Re: Equilibration

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
------------------------------------------------------------------------------------------------------

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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