From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Apr 24 2006 - 14:21:22 CDT
Dear Javier,
if you set up a simulation with langevin dynamics but without pressure
controls, it will be in the NVT ensemble. For example, the following is
a modification of the ubiquitin equilibration file from the namd
tutorial to be in the NVT ensemble:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../common/ubq_wb.psf
coordinates ../common/ubq_wb.pdb
set temperature 310
set outputname ubq_wb_eq
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 42. 0. 0.
cellBasisVector2 0. 44. 0.
cellBasisVector3 0. 0 47.
cellOrigin 31. 29. 17.5
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
#Note the lack of langevinpiston, which is the pressure control
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
reinitvels $temperature
run 2500 ;# 5ps
Lechuga, Javier wrote:
>Hello,
>
>In order to run a NVT ensemble with NAMD, I would like to know if someone can tell me about any NVT configuration files to get me started.
>
>Thank you
>
>
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