From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Oct 08 2006 - 13:37:16 CDT
For minimization, you should watch the force gradient values being
reported under the GRADIENT TOLERANCE headings in the namd output;
usually getting under 0.5 or so is good for minimization. Once you get
into equilibration, one measure of having an equilibrated system if
you're doing NVE simulations is to see when the temperature stabilizes;
there are others that are more appropriate for the types of simulations
usually done with NAMD (such as RMSD-based tests), since we usually use
a thermostat, and thus having a stable temperature is obviously not a
sign of equilibration. You may wish to consult an MD book like Leach's
"Molecular Modeling: Principles and Applications" for more on these points.
Dhiraj Srivastava wrote:
> 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
> <mailto: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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