From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Nov 15 2016 - 08:10:57 CST
Dear Richard,
There is no reason to use fixedAtoms with graphene, assuming you
generate the graphene structure with angles and dihedrals. My group
has a tutorial on simulations with graphene:
http://jeffcomer.us/tutorials.html
There is also some discussion of the effect of restraints in the SI of
our paper on free energy calculations on graphene:
http://dx.doi.org/10.1021/acsnano.5b03592
Regards,
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us
On Mon, Nov 14, 2016 at 3:03 PM, Richard Overstreet
<roverst_at_g.clemson.edu> wrote:
> 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