From: Shambo Hore (shambo.hore88_at_gmail.com)
Date: Sun May 22 2016 - 10:37:52 CDT
Hello, I am trying to simulate SMD tutorial file ubq_ww_pcv. as describe in
"
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node18.html
"
my configure namd file
>>>
>>>
>>>
structure ubq.psf
coordinates ubq_ww_eq.pdb
outputName ubq_ww_pcv
set temperature 310
# Periodic Boundary conditions
cellBasisVector1 20.0 0 0
cellBasisVector2 0 20.0 0
cellBasisVector3 0 0 50.0
cellOrigin 0 0 0
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 ;
langevinDamping 1 ;
(gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;
bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure yes ;
useFlexibleCell no ;
useConstantArea no ;
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
restartfreq 500 ;
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
# IMD Settings (can view sim in VMD)
IMDon on
IMDport 3000 ;
IMDfreq 1 ;
IMDwait no ;
SMD on
SMDFile ubq_ww_eq-ref.pdb
SMDk 7
SMDVel 0.005
SMDDir 0.3524 0.4021 0.845
SMDOutputFreq 10
run 20000 ;# 100ps
>>>
>>>
>>>
I have load the config file from NAMDgui.
When i run the simulation its running without giving any error, but in the
output log their were no sign of SMD simulation process.
as the tutorial file [namd tutorial : 3-1-pullcv] output log caontain :
( Info: FIXED ATOMS ACTIVE
Info: SMD ACTIVE
Info: SMD VELOCITY 0.005 ANGSTROM/TIMESTEP
Info: SMD DIRECTION 0.352418 0.402121 0.845044
Info: SMD K 7
Info: SMD OUTPUT FREQUENCY 10 TIMESTEPS
Info: SMD FILE ../common/ubq_ww_eq.ref)
When I run the same configuration file [ubq_ww_pcv.conf], but no such SMD
output in log file.
My package VMD:1.9.2, NAMD: NAMD_2.11_Win64-multicore;
Is there any solution or suggestion for fixing this problem.!!
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:10 CST