# AW: Re: Equilibration

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jun 29 2011 - 01:39:13 CDT

Hi,

maybe you should check if your total energy after minimization is really in
minimum. Maybe plot the total energy against the timestep and see if the
energy converges. The fact that especially the vdw energy goes to
9999999999.9999 indicates that atoms are too close to each other. Have you
fixed some atoms during minimization? If so, check if there's nothing going
wrong, and all atoms can get their right distances. Because the bond, angle
and dihed energy look fine, I think it is really just a problem of atoms
lying to close.

Best regards

Norman Geist.

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von bharat gupta
Gesendet: Mittwoch, 29. Juni 2011 08:06
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Re: Equilibration

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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