From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Oct 08 2006 - 12:13:26 CDT
Hi Dhiraj,
this is not a *problem* at all, but is by design. When you run
minimization, the system is brought toward a local minimum in the
potential energy surface using non-dynamics methods, so there will be no
temperature or kinetic energy present.
Peter
Dhiraj Srivastava wrote:
> Hi all
> when i am minimizing my protein in water box, i am getting zero
> kinetic energy, zero temperature and zero boundary. what may be the
> reason and how to solve this problem. my configuration file is
>
> ############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # Ubiquitin in a Water Sphere
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../common/prodh_wb.psf
> coordinates ../common/prodh_wb.pdb
>
> set temperature 310
> set outputname prodh1_min
>
> if {0} {
> set inputname prodh_min
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.xsc
> }
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_lipid.inp
> 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
>
> # Periodic Boundary Conditions
> cellBasisVector1 -81.875 0. 0.
> cellBasisVector2 0. -79.3840036392 0.
> cellBasisVector3 0. 0 -81.5929965973
> cellOrigin 5.72501993179 45.225315094 49.4890518188
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 82
> PMEGridSizeY 80
> PMEGridSizeZ 82
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 250
> outputPressure 250
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> #les off
> #lesFactor 10
> #lesReduceTemp on
> #lesReduceMass on
> #lesCol B
>
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 5000
> #reinitvels $temperature
> #run 500000 ;# 1000 ps
>
>
>
>
> Thank you in advance for help.
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
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