From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sat Oct 14 2006 - 21:55:15 CDT
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
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