From: patrick wintrode (pat_wde2_at_yahoo.com)
Date: Wed Feb 15 2006 - 15:51:55 CST
Thanks for the sample script.
Is this tcl script or a regular .conf file? I'm running this as a batch job on a remote machine. Will NAMD automatically recognize tcl commands in the configuration file?
Thanks again.
Patrick L. Wintrode
surendra negi <negi009_at_yahoo.com> wrote: Try to use following procedure.. change the paramter
marked with xxx and also minimization as well as MD
steps as per your requirement. I hope this will work.
surendra
------------
#
# Input files
set MOL solvated
structure ${MOL}_ionised.psf
#after minimization
set inprot ${MOL}_ionised_min
coordinates ${inprot}.coor
extendedSystem ${inprot}.xsc
# Input Force-Field Parameters
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
#
# Output files & writing frequency for DCD
# and restart files
#
outputname output/solvated_heat_out
binaryoutput off
restartfreq 1000
binaryrestart yes
dcdFile output/solvated_heat_out.dcd
#
# Frequencies for logs and the xst file
#
outputEnergies 1000
outputTiming 1000
outputPressure 1000
xstFreq 1000
dcdFreq 1000
#
# Timestep & friends
#
timestep 2.0 ;# 2fs/step
nonbondedFreq 2
rigidBonds all
rigidTolerance 0.00000001
fullElectFrequency 4
stepspercycle 20
#
# Simulation space partitioning
#
switching on
switchDist 10
cutoff 12
pairlistdist 13.5
#
# Basic dynamics
#
temperature 0
COMmotion no
dielectric 1.0
exclude scaled1-4
1-4scaling 1.0
#
# Particle Mesh Ewald parameters.
#
PME yes
PMEGridSizeX xx
PMEGridSizeY xx
PMEGridSizeZ xx
#
# Periodic boundary things
#
wrapWater on
wrapNearest on
wrapAll on
margin 1
cellBasisVector1 xx 0. 0.
cellBasisVector2 0. xx 0.
cellBasisVector3 0. 0. xx
cellOrigin xx xx xx
#
# Fixed atoms for initial heating-up steps
#
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol B
#
# Restrained atoms for initial heating-up steps
#
constraints on
consRef restrain_ca.pdb
consKFile restrain_ca.pdb
consKCol B
#
# Langevin dynamics parameters
#
langevin on
langevinDamping 10
langevinTemp 310 #
langevinHydrogen on
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310 #
useGroupPressure yes
# The actual minimisation and heating-up
# run one step to get into scripting mode
minimize 0
# turn off pressure control until later
langevinPiston off
# minimize nonbackbone atoms
minimize 100000 ;#
output output/min_fix
#
# min all atoms
#
fixedAtoms off
minimize 100000 ;#
output output/min_all
#
# heat with Ps restrained
#
set temp 10;
while { $temp < 311 } { ;#
langevinTemp $temp
run 5000 ;#
output output/heat_P
set temp [expr $temp + 31]
}
#
# equilibrate volume with Ps restrained
#
langevinPiston on
run 100000 ;#
output output/equil_P
#
# equilibrate volume without restraints
#
constraintScaling 0
run 100000 ;#
--- patrick wintrode
wrote:
> Hi all,
>
> I'm trying to minimize my system and then slowly
> heat it to 310 degrees C. After 2000 minimization
> steps I run dynamics for 10,000 steps. The
> temperature is set to 0 and langevin dynamics and
> langevin piston are both turned off.
>
> My heating protocol is
>
> reassignFreq 200
> reassignTemp 0
> reassignIncr 31
> reassignHold 310
>
> However, instead of slowing heating up in 31 degree
> increments, velocities are reassigned straight to
> 310 degrees at the first dynamics step.
>
> Anyone have an idea of what I'm doing wrong?
>
> Thanks.
>
> Patrick L. Wintrode
> Assistant Professor
> Department of Physiology & Biophysics
> Case Western Reserve University
>
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