AW: NPT with graphene

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Nov 15 2016 - 03:04:09 CST

The high energies result from fixedatoms+NPT, nothing to do with graphene. This is a result of atoms getting "rescaled into" the fixed atoms. Therefore excludefrompressure will not help here. What will help is to increase the barostat fluctuation timesteps in order to allow the system to relax after the rescaling for long enough. So try:

langevinpistondecay 1000
langevinpistonperiod 2000

Best wishes

Norman Geist

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Richard Overstreet
> Gesendet: Montag, 14. November 2016 22:04
> An: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: NPT with graphene
>
> To answer my own question. Turns out namd is actually ignoring these
> options.
>
> Warning: The following variables were set in the
> Warning: configuration file but will be ignored:
> Warning: excludeFromPressureFile (excludeFromPressure)
> Warning: excludeFromPressureCol (excludeFromPressure)
> Warning: fixedAtomsFile (fixedatoms)
> Warning: fixedAtomsCol (fixedatoms)
>
> I'll compile namd 2.12 looks like this was added to the GPU code on
> version 2.11.
>
>
> On 11/14/2016 12:29 PM, Richard Overstreet wrote:
> > NAMD Users,
> >
> > I am attempting to model protein adsorption on periodic graphene under
> > the NPT ensemble in namd with the langevin barostat. I have successfully
> > run NVT simulations for this system before however the barrostat is
> > producing high energies during the simulation run (4e6 kcal/mol). After
> > some testing I have determined graphene combined with the langevin
> > barostat produces high energies in the simulation. In an attempt to
> > prevent this I enabled the "useConstantArea" and "ExcludeFromPressure"
> > options however total energies for this simulation remain high. I
> > assumed that excluding the graphene atoms from the pressure calculation
> > would prevent the scaling of those atomic coordinates and using a
> > flexible cell with a constant area would only scale the PBC box in the Z
> > dimension but this does not appear to be the case. In each instance the
> > barostat appears to be compressing the graphene monolayer producing
> > energies on the order of 4e6-5e6 kcal/mol. Not sure why namd is ignoring
> > these options unless I am not implementing the barostat correctly. As a
> > final note the graphene atoms remain fixed during the simulation using
> > the "fixedAtoms" option. Any advice is appreciated.
> >
> > Regards,
> >
> > Richard Overstreet
> >
> >
> > #############################################################
> > ## ADJUSTABLE PARAMETERS ##
> > #############################################################
> >
> > structure ./insconfig_tip3_autopsf.psf
> > coordinates ./ins_ads_e.coor
> > velocities ./ins_ads_e.vel
> >
> > set itemp 300
> > set ftemp 300
> > set outputname ins_ads_p
> >
> > firsttimestep 0
> >
> >
> > #############################################################
> > ## SIMULATION PARAMETERS ##
> > #############################################################
> >
> > # Input
> > paraTypeCharmm on
> > parameters ./graphene_par_all27_prot_na.prm
> >
> >
> >
> > # Force-Field Parameters
> > exclude scaled1-4
> > 1-4scaling 1.0
> > cutoff 12.0
> > switching on
> > switchdist 10.0
> > pairlistdist 14.0
> >
> > # Heating parameters
> > #temperature $itemp
> > #rescaleFreq 1
> > #rescaleTemp $ftemp # The value of temperature to be kept after heating
> > is completed
> >
> > #Pressure Paramters
> > langevin on
> > langevinTemp $ftemp
> > LangevinPiston on
> > LangevinPistonTarget 1.01325
> > LangevinPistonPeriod 200
> > LangevinPistonDecay 100
> > LangevinPistonTemp $ftemp
> > useFlexibleCell yes
> > useConstantArea yes
> >
> > # Integrator Parameters
> > timestep 1.0
> > rigidBonds all
> > nonbondedFreq 1
> > fullElectFrequency 1
> > stepspercycle 10
> >
> > # Periodic Boundary Conditions
> > cellBasisVector1 105.86000229644776 0.0 0.0
> > cellBasisVector2 0.0 105.98900129127503 0.0
> > cellBasisVector3 0.0 0.0 204.62000347900391
> > cellOrigin 48.24700117111206 48.39250075817108
> 101.60100173950195
> >
> > wrapAll on
> >
> > # PME (for full-system periodic electrostatics)
> > PME yes
> > PMEGridSpacing 0
> >
> > #manual grid definition
> > PMEGridSizeX 108
> > PMEGridSizeY 108
> > PMEGridSizeZ 408
> >
> > # Output
> > outputName $outputname
> >
> > restartfreq 500 ;# 500steps = every 1ps
> > dcdfreq 250
> > xstFreq 250
> > outputEnergies 100
> >
> > #############################################################
> > ## EXTRA PARAMETERS ##
> > #############################################################
> >
> > binaryrestart no
> > binaryoutput no
> >
> > fixedAtoms on
> > fixedAtomsFile ./insconfig_tip3_43.300.pdb
> > fixedAtomsCol B
> >
> > ExcludeFromPressure on
> > ExcludeFromPressureFile ./insconfig_tip3_43.300.pdb
> > ExcludeFromPressureCol B
> >
> >
> > #############################################################
> > ## EXECUTION SCRIPT ##
> > #############################################################
> >
> > # Minimization
> >
> > numsteps 1000000 ;# 2ns
> >
> >
> > ################################OUTPUT###############
> >
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP ELECT VDW BOUNDARY
> > MISC KINETIC TOTAL TEMP
> > POTENTIAL TOTAL3 TEMPAVG PRESSURE
> > GPRESSURE VOLUME PRESSAVG GPRESSAVG
> >
> > ENERGY: 0 30168.5163 3769037.4091 1132606.4435
> > 48.6455 -350132.3687 30823.4125 0.0000
> > 0.0000 58745.3058 4671297.3640 282.9142
> > 4612552.0582 4671498.1484 282.9142 -5843.9748
> > -5844.0621 2295835.6042 -5843.9748 -5844.0621
> >

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:48 CST