Re: Reassign Temp during the Production Run

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Thu Jul 16 2009 - 12:17:02 CDT

Um.....yeah.

What property do you want to measure from the multi-temp simulation?

Chris

--
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 Thu, Jul 16, 2009 at 12:04 PM, twshen <tshen_at_uh.edu> wrote:
> Dear all,
>
>  I found that I reassign the temperature, in other words,
> velocities, every 500 steps during the production run.
> Since "reassignTemp" should be turned off during the
> production run, I am wondering if this can make a
> difference in the trajectory. Thank you very much.
>
> Here are my simulation parameters for the production run,
>
> # Input
> paraTypeCharmm      on
> parameters               toppar/par_all27_prot_na.prm
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff                 12.0
> switching           on
> switchdist          10.0
> pairlistdist         13.0
> margin               2.5
>
> # Integrator Parameters
> timestep            2.0  ;# 2fs/step
> rigidBonds          all  ;# needed for 2fs steps
> nonbondedFreq       1    ;# nonbonded forces calculated every step
> fullElectFrequency  1    ;# elect (PME) calculated every step
> stepspercycle       10
>
> # Reassign velocities
> reassignFreq        500
> reassignTemp        310
>
> # Periodic Boundary Conditions (PBC) (cellorigin = center of the cell)
> cellBasisVector1   107.00   0.0      0.0
> cellBasisVector2     0.0   98.0      0.0
> cellBasisVector3     0.0    0.0     94.0
> cellOrigin           0.0    0.0      0.0
> wrapWater            on
> wrapAll              on
> wrapNearest          on
>
> # PME (for full-system periodic electrostatics)
> PME                  yes
> PMEGridSizeX         120
> PMEGridSizeY         100
> PMEGridSizeZ          96
>
>
> # Constant Pressure and Temperature Control (variable volume)
> tCouple              on
> tCoupleTemp          310
> useGroupPressure     yes ;# needed for rigidBonds
> useFlexibleCell      no
>
> BerendsenPressure                  on
> BerendsenPressureTarget            1.01
> BerendsenPressureCompressibility   0.000049
> BerendsenPressureRelaxationTime    500
> BerendsenPressureFreq              20
>
>

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