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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