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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