Re: Equilibration

From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Wed Jun 29 2011 - 01:06:10 CDT

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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