From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Tue Sep 13 2016 - 15:39:42 CDT
Dave,
Thank you for the explanations! I found that my equilibration process had
left my system in a state in which some atoms were overlapping, so I am
going back to fix that step first. Then I will come back to this step and
follow the instruction you gave me here.
Thanks Again!
Jack
On Tue, Sep 13, 2016 at 2:13 PM, Hardy, David Joseph <dhardy_at_illinois.edu>
wrote:
> Dear Jack,
>
> You are mixing various protocols in your simulation that don't make sense
> together. You have constant temperature and constant pressure running
> together with your heating protocol. First, you should get rid of the
> thermostat and barostat, as they are working against your heating
> protocol. Also, the fatal error you are seeing is likely due to the
> barostat, so that should go away. Second, your reassignFreq and
> reassignIncr choices are too small. Keep in mind that a temperature
> reassignment is setting random velocities (to that temperature) for all of
> your atoms, but this suggests that your system will require some number of
> steps to "settle down." More typically, you would change the temperature
> using a bigger increment and allow the system to equilibrate to that new
> temperature over, say, 100 to 1000 steps. So as a smallest increment, try
> reassignFreq 200 and reassignIncr 1, or maybe better try larger increments
> of reassignFreq 1000 and reassignIncr 5.
>
> Best regards,
> Dave
>
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois
> dhardy_at_illinois.edu
> http://www.ks.uiuc.edu/~dhardy/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_-7Edhardy_&d=CwMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=GWAjb9a33GjTI8MGzbUGGaYnDpRx4Zh4AiwAlO3IZd4&m=bl8B_9xNnCVuRSWQIQ5lNV6zQ8HjBToZ-0b1LcXP9Dg&s=Cl9GKOa5FAIjZySaJOXACvrTt13thJb_gQ9ENqVdUfE&e=>
>
>
> On Sep 13, 2016, at 8:34 AM, Jackson Cavett <jcavett_at_mail.bradley.edu>
> wrote:
>
> Hello NAMD Users,
>
> I am attempting to heat a molecule from 10K to 310K over the course of a
> few simulations. I put in the following parameters to accomplish this
> heating:
>
> reassignFreq 2
> reassignTemp 10
> reassignIncr 0.01
> reassignHold 60
>
> However, when I run the simulation, I get the periodic boundary error on
> the first timestep. Here is the log file which shows the problem:
>
> REINITIALIZING VELOCITIES AT STEP 100000 TO 10 KELVIN.
> TCL: Running for 10000 steps
> REASSIGNING VELOCITIES AT STEP 100000 TO 60 KELVIN.
> PRESSURE: 100000 110.253 -0.316211 -6.80342 -0.316211 126.441 1.37312
> -6.80342 1.37312 145.667
> GPRESSURE: 100000 116.487 -0.516909 -5.56659 0.0868719 131.886 1.15381
> -5.4699 1.44817 149.358
> ETITLE...
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> REASSIGNING VELOCITIES AT STEP 100002 TO 60 KELVIN.
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> I don't understand why the temperature is being reassigned to 60K when I
> stated that it should be reassigned to 10K every two timesteps. Can anyone
> explain what is happening here?
>
> Here is the full configuration file I used. Please note what I did with
> the binVelocities. I'm not sure if I can comment them out like that when I
> use a restart file, so please let me know what I should do with that. The
> reason I comment it out is that I want to set the temperature of my
> simulation while still using a restart file.
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Equilibration of alphVbeta3 after minimization
> # Shorter simulations so dcd can be analyzed
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../alphaVbeta6_wb.psf
> coordinates ../alphaVbeta6_wb.pdb
>
> set temperature 10
> set outputname beta6_equil_1
>
> # Continuing a job from the restart files
> if {1} {
> set inputname ../minimization/beta6_min_fixed_protein
> binCoordinates $inputname.restart.coor
> #binVelocities $inputname.restart.vel
> extendedSystem $inputname.xsc
> }
>
> firsttimestep 100000
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../par_all27_prot_lipid.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1. ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 121 0.0 0.0
> cellBasisVector2 0.0 93 0.0
> cellBasisVector3 0.0 0.0 57.5
> cellOrigin 20.045 -30.903 25.591
>
> wrapWater on
> wrapAll on
> wrapNearest off
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
> #manual grid definition
> #PMEGridSizeX 45
> #PMEGridSizeY 45
> #PMEGridSizeZ 48
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.0
> langevinPistonDecay 50.0
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 1000 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 200
> outputPressure 200
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> #For heating, use temperature reassignment
> reassignFreq 2
> reassignTemp 10
> reassignIncr 0.01
> reassignHold 60
>
> # Minimization
> #minimize 10000
> #reinitvels $temperature
>
> reinitvels $temperature
> run 10000 ;#
>
>
> Thank you all for your help!
>
> Jack
>
>
>
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