Re: Re: Equilibration

From: saman amiri (
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 <> To: 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 :

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