From: david gae (ddgae_at_ucdavis.edu)
Date: Tue Sep 13 2016 - 12:03:07 CDT
Jack,
I can only suggest small minor things as I don’t know anything about your project or your system. I suggest you talk with an expert at your university about what you would like to do.
temperature increase 0.01 seems really small to me. But reassign incr does use decimals (just read it in the namd manual). Also you might want to consider using margin as the previous person stated.
Furthermore, you also might want to use minimized output coordinate of your system and measure the size of your system. And use that as your PME grid size.
I hope this helps,
David
> On Sep 13, 2016, at 8:32 AM, Jackson Cavett <jcavett_at_mail.bradley.edu> wrote:
>
> David,
>
> What I am hoping to do is increase the temperature very slowly from 10 to 60K, then from 60K to 110K, from 110K to 160K and so on until I get to 310K. So my plan is to run 6 10,000-timestep simulations in order to heat up my system before equilibration. The second attempt (shown in the second email) looked like it was going to do this until the periodic boundary error. I will try to update the PME boundary and see what that does. How exactly should I go about doing this? I really appreciate your help!
>
> Thanks,
>
> Jack
>
> On Tue, Sep 13, 2016 at 9:27 AM, david gae <ddgae_at_ucdavis.edu <mailto:ddgae_at_ucdavis.edu>> wrote:
> Hi Jackson,
>
> I’m no expert in MD, others are better at explaining this than I am.
>
> but are you holding temperature of your system to 60K then using the output coordinate/freq for additional heatup from 60K to 310K?
> I would change reassignHold to 310
> and reassignIncr to sometime like 5?
>
> maybe reassignIncr doesn’t understand floating point values, you probably need to use whole number for temperature reassignment. I used whole numbers in the past.
>
> if this is not the cause of your problem, you might want to manually assign the PME boundary for electrostatics.
>
> All the best,
> David
>
> > On Sep 13, 2016, at 6:34 AM, Jackson Cavett <jcavett_at_mail.bradley.edu <mailto: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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