Re: Re: Equilibration

From: saman amiri (saman_amiri00_at_yahoo.com)
Date: Thu Jun 30 2011 - 02:53:42 CDT

Regarding timestep decreasing, No, because it is only related to the MD calculation not for the minimization step. Regarding the trick, I do not know what you exactly mean. The trick is about minimization. Your minimization steps and dcdfreq are 50000 and 250, respectively. Therefore, you should have a lot of frames even for the minimization process. Then I recommend you to follow the trick using the final snapshot of minimization.  Please also consider whether you have set the PBC parameters, correctly. let me know if you have further questions. ________________________________ From: bharat gupta <bharat.85.monu_at_gmail.com> To: saman amiri <saman_amiri00_at_yahoo.com> Sent: Thursday, June 30, 2011 4:10 AM Subject: Re: namd-l: Re: Equilibration Hi, I want to ask can we do this what you said in your mail, for the minimization step. As after loading the psf file and then the .dcd file the number of frames doesnot  increase in my case. Here are the minimization parameters that I am using:- ## JOB DESCRIPTION                                         ## ############################################################# # Minimization and Equilibration  ############################################################# ## ADJUSTABLE PARAMETERS                                   ## ############################################################# structure          ../common/complex_ionized.psf coordinates        ../common/complex_ionized.pdb set temperature    298 set outputname     complex_minim firsttimestep      0 ############################################################# ## SIMULATION PARAMETERS                                   ## ############################################################# # Input paraTypeCharmm    on parameters          ../common/par_all27_prot_na.prm  # you may need to specify a path temperature         $temperature # Force-Field Parameters exclude             scaled1-4 1-4scaling          1.0 cutoff              12. switching           on switchdist          10. pairlistdist        13.5 # Integrator Parameters timestep            2.0  ;# 2fs/step rigidBonds          all  ;# needed for 2fs steps nonbondedFreq       1 fullElectFrequency  2   stepspercycle       10 # Constant Temperature Control langevin            on    ;# do langevin dynamics langevinDamping     5     ;# damping coefficient (gamma) of 5/ps langevinTemp        $temperature langevinHydrogen    off    ;# don't couple langevin bath to hydrogens # Output outputName          $outputname restartfreq         500     ;# 500steps = every 1ps dcdfreq             250 outputEnergies      100 outputPressure      100 ############################################################# ## PBC PARAMETERS                                        ## ############################################################# # Periodic Boundary Conditions cellBasisVector1     62.4   0.0   0.0 cellBasisVector2     0.0    51.6   0.0 cellBasisVector3     0.0    0.0   46.6 cellOrigin           8.3    69.6   -10.1 ############################################################# ## EXECUTION SCRIPT                                        ## ############################################################# # Minimization minimize            50000 reinitvels          $temperature run 50000 ;# 100 ps On Thu, Jun 30, 2011 at 6:05 AM, saman amiri <saman_amiri00_at_yahoo.com> wrote: Hi Bharat, > > >As you can see, vdW interaction energy is out of order. The error is coming from too closeness of some atoms relative to each other. Upon finishing the minimization process, MD is crashed due to high velocity of those atoms which their Cartesian positions are too close to each other. Such an error is common when there are some coincidence of atoms position in the initial coordination file (pdb file). > >There are some ways to deal with the problem. One way is increasing minimization steps, but since minimization through 20000 steps is enough (I think), I recommend you to use the following trick: > > >load the psf as well as final snapshot of your MD simulation. and then select those atoms which have a high velocity. > > >set qwe [atomselect top "Write the controversial atoms index"] >$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 > > > -- 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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