From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Tue Sep 13 2016 - 09:01:43 CDT
I changed the first timestep to 0, but I am still getting the same error.
My new output looks like:
REINITIALIZING VELOCITIES AT STEP 0 TO 1 KELVIN.
TCL: Running for 10000 steps
REASSIGNING VELOCITIES AT STEP 0 TO 1 KELVIN.
PRESSURE: 0 88.5268 -0.275966 -6.30021 -0.275966 104.791 1.31692 -6.30021
1.31692 123.292
GPRESSURE: 0 94.5003 -0.497417 -5.30475 0.106364 109.591 1.24966 -5.20806
1.54402 127.56
ETITLE:...
OPENING EXTENDED SYSTEM TRAJECTORY FILE
REASSIGNING VELOCITIES AT STEP 2 TO 1.01 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.
So this seems to have helped the temperature reassignment, but I am still
running into the periodic boundary error. Does anyone have any suggestions?
Thank You,
Jack
On Tue, 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
>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:27 CST