From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Mon Nov 14 2016 - 15:03:43 CST
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
>
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