From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Mon Jun 06 2011 - 07:02:41 CDT
Sorry,
A problem with my copy and paste
Here the complet script.
Regards,
Flavio
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Simulated annealing
#############################################################
## ADJUSTABLE
PARAMETERS ##
#############################################################
structure PROT.psf
coordinates PROT.pdb
set temperature 300
set outputname PROT_anneal
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
#
Input
paraTypeCharmm on
parameters par_all27_prot_lipid_na.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 1.0 ;# 1fs/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 85.5 0. 0.
cellBasisVector2 0. 100. 0.
cellBasisVector3 0. 0.
75.5
cellOrigin 74.5 58.0 65.0
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 90
#PMEGridSizeY 105
#PMEGridSizeZ 80
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston
on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
binaryoutput no
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA
PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
for { set TEMP 0 } { $TEMP < 300 } { incr TEMP 5 } {
run 20000
reassignTemp $TEMP
}
minimize 1000
--- On Sat, 6/4/11, Molecular Dynamics
<moleculardynamics_at_yahoo.com> wrote:
From: Molecular Dynamics <moleculardynamics_at_yahoo.com>
Subject: Re: namd-l: conf file script ( help needed )
To: "flavio seixas" <oivalf_nix_at_yahoo.com>
Date: Saturday, June 4, 2011, 9:39 PM
Dear Flavio,
Thanks for the script and I will try it for my simulations, but I think some parts of the script is missing and it 's not complete. So could you please re-send your script ?
Thanks for your help
M
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