From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 17 2009 - 20:51:03 CDT
Hi Marcelo,
in your config file, you appear to be setting the initial reassignTemp
to 300 K (since that is what $temperature is set to).
Also, you need to either turn off the Langevin piston or manually update
its temperature as well.
Best,
Peter
Marcelo Puiatti wrote:
> Dear all:
>
> I'm trying to perform a couple of MD runs varying the temperature from
> 50 K to 300 K.
> I've read the manual and I add this lines to the config file:
>
> reassignFreq 100
> reassignTemp $temperature
> reassignIncr 5
> reassignHold 300
>
>
> but after I read the output file with the Namd-plot pluggin with VMD
> the system is always at the final temperature.
>
> I'll apreciate any help, I attached here a copy of my config file.
>
> Thank's in advance
>
> Marcelo
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> coordinates ../ntv.pdb
> outputName heat1
>
> set temperature 300
>
> # Continuing a job from the restart files
> if {1} {
> set inputname min-3
> binCoordinates $inputname.restart.coor
> # binVelocities $inputname.restart.vel ;# remove the
> "temperature" entry if you use this!
> extendedSystem $inputname.restart.xsc
> }
>
> firsttimestep 2500
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
>
> paraTypeCharmm off
> paratypeXplor off
> amber on
> parmfile ../adri.top
> ambercoor ../adri.crd # chequear
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> temperature $temperature
>
>
> # Periodic Boundary Conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {0} {
> cellBasisVector1 25. 0. 0.
> cellBasisVector2 0. 25.3 0.
> cellBasisVector3 0. 0. 24.3
> cellOrigin -0.14 0.40 -0.39
> }
> wrapWater on
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics)
> if {0} {
> PME yes
> PMEGridSizeX 32
> PMEGridSizeY 32
> PMEGridSizeZ 32
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> # Escalar la temperatura de 0 K a 300K
> reassignFreq 100
> reassignTemp $temperature
> reassignIncr 5
> reassignHold 500
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no
> useConstantArea no
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
>
> restartfreq 1000 ;# 1000steps = every 1ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 100
> outputPressure 100
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsFile nottails.fix.pdb
> fixedAtomsCol B
> fixedAtomsForces on
> }
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
> constraints on
> consexp 3
> consref ../adri-ntv.pdb
> conskfile ../adri-ntv.pdb
> conskcol O
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {0} {
> minimize 1000
> reinitvels $temperature
> }
>
> run 50000 ;# 0.050 ns
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:55 CST