From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Sep 13 2016 - 09:15:38 CDT
Hi!
As it says in the error, try to increase the margin, for example by
including
margin 3
in the configuration file.
Best,
Ajasja
On 13 September 2016 at 16:01, Jackson Cavett <jcavett_at_mail.bradley.edu>
wrote:
> 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
>>
>
>
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