Re: error during heating of the minimized system: (please reply!)

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Jan 14 2009 - 23:11:31 CST

You are heating your system. This increases the velocities on the atoms.
RATTLE and a timestep greater than 1.0 should generally not be used when
heating a system. Set your timestep to 1.0 and change "rigid all" to "rigid
water". Heat your system, equilibrate, then try to switch back to timestep
2.0 and "rigid all."

C.

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Wed, Jan 14, 2009 at 1:08 AM, Falgun Shah <fhshah_at_olemiss.edu> wrote:
> Dear sir
>
> i am doing minimization and equilibration of protein of interest. I have
> minimized sysem for 1500 steps of CG minimization using backbone and calpha
> atom fixed
>
> In following step, i want to heat the system in increment (0 to 300k for
> 3000 steps: 100K for 1000steps). i am getting following error:
>
> ERROR: Step 130 cell rescaling factor limited.
> ERROR: Constraint failure in RATTLE algorithm for atom 2822!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
>
> I am pasting my configuration file
>
> #############################################################
> ## ADJUSTABLE PARAMETERS                                   ##
> #############################################################
>
> structure          junk_wb_ionized.psf
> coordinates        junk_wb_min_calpha2_eq.coor
>
> set temperature    0
> set outputname     junk_wb_heat_calpha_eq
>
> set temp_step      20
> firsttimestep      0
>
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
>
> # Input
> paraTypeCharmm        on
> parameters
> /home/Amber9.0/NAMD_2.6_Linux-amd64/namd-tutorial-files/common/par_all27_prot_lipid.inp
>
> temperature         $temperature
>
> # Periodic Boundary Conditions
> #
> if {1} {
> cellBasisVector1    95.4   0.    0.
> cellBasisVector2     0.   75.58   0.
> cellBasisVector3     0.    0.   65.72
> cellOrigin          10.2   1.2   1.3
> }
> wrapWater           on
> wrapAll             on
>
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              13.
> switching           on
> switchdist          11.
> pairlistdist        14.5
>
>
> # Integrator Parameters
> timestep            2.0  ;# 2fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       20
>
> # PME (for full-system periodic electrostatics)
> if {1} {
> PME                 yes
> PMEGridSizeX        125
> PMEGridSizeY        81
> PMEGridSizeZ        64
> }
>
> # temp rescaling actually brings the temp down
> # thats why perform incremental heating
>
> if {1} {
> reassignTemp         $temp_step ;#starting temp
> reassignIncr         $temp_step ;#temp increment
> reassignHold         300        ;#final temp
> reassignFreq         100        ;#num timestep to temp incr.
>
>
> # Constant Temperature Control
> #langevin            off    ;# do langevin dynamics
> #langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
> #langevinTemp        $temperature
> #langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
>
>
> # Use BerendsenPressure Control to equilibrate
> if {1} {
> useGroupPressure      yes ;# needed for rigidBonds
> useFlexibleCell       no
> useConstantArea       no
>
> BerendsenPressure                 on
> BerendsenPressureTarget           1.01325 ;#  in bar -> 1 atm
> BerendsenPressureCompressibility  4.57E-5
> BerendsenPressureRelaxationTime   200
> BerendsenPressureFreq             20
> }
>
> # Output
> outputName          $outputname
>
> restartfreq         500     ;# 500steps = every 1ps
> dcdfreq             250
> xstFreq             250
> outputEnergies      50
> outputPressure      100
> binaryoutput        no    ;# give me the pdb instead of the .coor
>
>
> #############################################################
> ## EXTRA PARAMETERS                                        ##
> #############################################################
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {1} {
> fixedAtoms          on
> fixedAtomsFile      junk_fixed_calpha_atoms.pdb
> fixedAtomsCol       B
> fixedAtomsForces    off
> }
>
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
>
> # Minimization
> if {1} {
> minimize            100
> reinitvels          $temperature
> }
> run 3000 ;# 5ps
>
> Please let me know if there is any error in my configuration file.
>
> Thanks
> --
> Falgun H shah
> PhD candidate (3rd year)
> Department of Medicinal Chemistry
> 2028, Natural Product Center
> University of Mississippi
>
> Ph No: 6629151286(O)
>           662 801 5667(M)
> email: fhshah_at_olemiss.edu
>

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