From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sun Oct 08 2006 - 12:23:31 CDT
Hi Peter
So how should i check whether my system is minimized or not. i was thinking
that its a good check to ensure the minimization if the temperature get
constant during simulation. is it for minimization or for equilibration. i
am little bit confuse about this. thank you for your help.
Dhiraj
On 10/8/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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
>
>
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
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