Re: problem with reassigning temperature

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sun Oct 15 2006 - 14:08:31 CDT

Hi Jerome
thank you for your help.
now i understand that when i remove the thermostat then velocity will
determine the temperature of the system which after minimization is
equivalent to 0 K. so should i remove the *constant temperature control*.
but then it will be NVE ensemble. is it correct to heat my system up to 310
K without Constant Temperature control? I am planning to run my simulation
in NVE ensemble.
Dhiraj

On 10/15/06, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
>
> Hi Dhiraj,
> Think about it that way: if you had no thermostat, what would determine
> the
> initial temperature of the system?
>
> Jerome
>
> On Saturday 14 October 2006 22:55, Dhiraj Srivastava wrote:
> > Hi all
> > I am trying to equilibrate my system at 310 K so i am using the
> > temperature reassignments parameter to gradually increase the
> temperature
> > of my system. but before that i have energy minimized structure for
> 10000
> > step. i am using the reassignment frequency of 1000 step. here is the
> > script.
> >
> > #############################################################
> > ## 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 5
> > set outputname prodh_wb_eq
> >
> > if {1} {
> > set inputname prodh_min_eq
> > binCoordinates $inputname.restart.coor
> > binVelocities $inputname.restart.vel ;# remove the "temperature"
> > entry if you use this!
> > extendedSystem $inputname.xsc
> > }
> >
> > firsttimestep 10000
> >
> >
> > #############################################################
> > ## 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 12.0
> > switching on
> > switchdist 10.0
> > 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 1 ;# 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 0.0
> > cellBasisVector2 0.0 -79.3840036392 0.0
> > cellBasisVector3 0.0 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 100
> > outputPressure 100
> >
> >
> > #############################################################
> > ## EXTRA PARAMETERS ##
> > #############################################################
> > constraints on
> > consexp 2
> > consref ../common/prodh_wb_ref.pdb
> > conskfile ../common/prodh_wb_res5.pdb
> > conskcol B
> >
> > reassignFreq 1000
> > reassignTemp 5
> > reassignIncr 5
> > reassignHold 310
> >
> > #############################################################
> > ## EXECUTION SCRIPT ##
> > #############################################################
> >
> > reinitvels $temperature
> > run 62000 ;# 600ps
> >
> >
> >
> > now the problem is that NAMD is starting the simulation at 55 K instead
> of
> > 5 K. I am thinking that perhaps it is reassigning the temperature at
> every
> > 1000 time step as the script says but since i have already energy
> minimized
> > the structure for 10000 time step so NAMD is also taking in to account
> > those time steps. how should I change my script so NAMD starts my
> > simulation at 5 K instead of at 55 K?
> >
> > Thank you.
>

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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