From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun Oct 15 2006 - 11:29:54 CDT
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.
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