SMD simulation problem.

From: Shambo Hore (shambo.hore88_at_gmail.com)
Date: Sun May 29 2016 - 20:15:57 CDT

Hello.
I am trying to simulate the SMD tutorial file. downloaded from
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/3-1-pullcv/

I have load the configuration file in NAMDgui.

my configuration :

outputName final
set temperature 310
coordinates ubq_ww_eq.pdb
structure ubq.psf
temperature $temperature

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

wrapWater on
wrapAll on

# 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

#PME (for full-system periodic electrostatics)

PME yes
PMEGridSpacing 1.0

# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

# Fixed Atoms Constraint (set PDB beta-column to 1)
fixedAtoms on
fixedAtomsFile ubq_ww_eq-ref.pdb
fixedAtomsCol B

SMD on
SMDFile ubq_ww_eq-ref.pdb
SMDk 7
SMDVel 0.005
SMDDir 0.3524 0.4021 0.845
SMDOutputFreq 10

--------------------------------------------

when i load this namd config file it gives a warning msg in TKconsol

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: wrapWater on
WARNING: ignoring command: wrapAll on
WARNING: ignoring command: rigidBonds all
WARNING: ignoring command: PME yes
WARNING: ignoring command: PMEGridSpacing 1.0
WARNING: ignoring command: langevin off
WARNING: ignoring command: langevinDamping 1
WARNING: ignoring command: langevinTemp 310
WARNING: ignoring command: langevinHydrogen no
WARNING: ignoring command: useGroupPressure yes
WARNING: ignoring command: useFlexibleCell no
WARNING: ignoring command: useConstantArea no
WARNING: ignoring command: langevinPiston on
WARNING: ignoring command: langevinPistonTarget 1.01325
WARNING: ignoring command: langevinPistonPeriod 100.
WARNING: ignoring command: langevinPistonDecay 50.
WARNING: ignoring command: langevinPistonTemp 310
WARNING: ignoring command: outputPressure 100
WARNING: ignoring command: fixedAtomsFile ubq_ww_eq-ref.pdb
WARNING: ignoring command: fixedAtomsCol B
WARNING: ignoring command: SMD on
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

-----------------------------

I have checked the SMD file, it is correct in beta and occupancy column.

though i carry the simulation it simulate without giving any error, but at
the end no smd simulation shown in log file.

Please find the actual problem and give a reasonable answer.

Thank you

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