Re: Re: Equilibration

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jun 29 2011 - 18:00:48 CDT

Try to reduce the solvation box size and repeat the simulation. This is how
i fixed this problem.

On Wed, Jun 29, 2011 at 4:05 PM, saman amiri <saman_amiri00_at_yahoo.com>wrote:

> 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
> 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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