From: saman amiri (saman_amiri00_at_yahoo.com)
Date: Wed Jun 29 2011 - 16:05:11 CDT
Hi Bharat,
As you can see, vdW interaction energy is out of order. The error is coming from too closeness of some atoms relative to each other. Upon finishing the minimization process, MD is crashed due to high velocity of those atoms which their Cartesian positions are too close to each other. Such an error is common when there are some coincidence of atoms position in the initial coordination file (pdb file).
There are some ways to deal with the problem. One way is increasing minimization steps, but since minimization through 20000 steps is enough (I think), I recommend you to use the following trick:
load the psf as well as final snapshot of your MD simulation. and then select those atoms which have a high velocity.
set qwe [atomselect top "Write the controversial atoms index"]
$qwe moveby {0.3 0.3 0.3}
set qaz [atomselect top all]
$qaz writepdb COOR.pdb
now use the new pdb file (COOR.pdb) along with the previous psf file. Note you should first run a minimization step for about 5000 steps.
if it dose not work, you have to decrease your timestep. Such an error is also common if you have atoms in your system with a high epsilon (for instance, Platinum and some other transition metals).
hope this information is useful.
Best,
Saman
________________________________
From: bharat gupta <bharat.85.monu_at_gmail.com>
To: namd-l_at_ks.uiuc.edu
Sent: Wednesday, June 29, 2011 10:36 AM
Subject: 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
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