From: Shambo Hore (shambo.hore88_at_gmail.com)
Date: Tue May 31 2016 - 12:11:35 CDT
Hello,
I am loading a preconfigure namd file in NAMDgui [ VMD 1.9.2 / NAMD :
NAMD_2.11_Win64-multicore ]. the configuration file named final.namd .
the configuration file contain :
coordinates ubq_ww_eq.pdb
structure ubq.psf
# output
set output final
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 500
xstFreq 500
binaryoutput yes
binaryrestart yes
outputEnergies 500
restartfreq 500
fixedAtoms on
fixedAtomsFile ubq_ww_eq-ref.pdb
fixedAtomsCol B
SMD yes
SMDFile ubq_ww_eq-ref.pdb
SMDk 7
SMDVel 0.005
SMDDir 0.3524 0.4021 0.845
SMDOutputFreq 10
# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
# Simulation space partitioning
switching on
switchdist 9
cutoff 10
pairlistdist 12
# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20
nonbondedFreq 2
fullElectFrequency 4
# Temperature control
set temperature 310
temperature $temperature; # initial temperature
# Langevin Dynamics
langevin on; # do langevin dynamics
langevinDamping 1; # damping coefficient (gamma) of
1/ps
langevinTemp $temperature; # bath temperature
langevinHydrogen no; # don't couple langevin bath to
hydrogens
seed 12345
# PBC
cellBasisVector1 30.0 0.0 0.0
cellBasisVector2 0.0 34.0 0.0
cellBasisVector3 0.0 0.0 35.0
cellOrigin 30.12 28.94 15.68
wrapAll yes
dcdUnitCell yes
PME yes
PMEGridSizeX 30
PMEGridSizeY 32
PMEGridSizeZ 36
# Scripting
minimize 2000
reinitvels $temperature
run 200000
---------------------------------------------
after loading the namd configuration file in NAMDgui it gives following
error in TKconsol,
WARNING: ignoring command: fixedAtomsFile ubq_ww_eq-ref.pdb
WARNING: ignoring command: fixedAtomsCol B
WARNING: ignoring command: SMD yes
WARNING: ignoring command: SMDFile ubq_ww_eq-ref.pdb
WARNING: ignoring command: SMDk 7
WARNING: ignoring command: SMDVel 0.005
WARNING: ignoring command: SMDDir 0.3524 0.4021 0.845
WARNING: ignoring command: SMDOutputFreq 10
WARNING: ignoring command: langevin on
WARNING: ignoring command: langevinDamping 1
WARNING: ignoring command: langevinTemp 310
WARNING: ignoring command: langevinHydrogen no
WARNING: ignoring command: seed 12345
WARNING: ignoring command: cellBasisVector1 30.0 0.0 0.0
WARNING: ignoring command: cellBasisVector2 0.0 34.0 0.0
WARNING: ignoring command: cellBasisVector3 0.0 0.0 35.0
WARNING: ignoring command: cellOrigin 30.12 28.94 15.68
WARNING: ignoring command: wrapAll yes
WARNING: ignoring command: dcdUnitCell yes
WARNING: ignoring command: PME yes
WARNING: ignoring command: PMEGridSizeX 30
WARNING: ignoring command: PMEGridSizeY 32
WARNING: ignoring command: PMEGridSizeZ 36
I have checked the fixed/smd atom, it set correct values in beta/occupancy
column.
Why this ignoring command generate regarding the configuration file?
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