From: Madhulika Gupta (gmadhulika1909_at_gmail.com)
Date: Sun May 22 2016 - 10:59:18 CDT
Hi,
Your output log file doesn't seem to contain no. of SMD atoms? Check if you
have correctly specified the occupancy column to be non zero for SMD atoms.
Best
Madhulika
On May 22, 2016 9:09 PM, "Shambo Hore" <shambo.hore88_at_gmail.com> wrote:
> 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