From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Jan 27 2015 - 13:22:38 CST
Dear Dawid,
You are applying a huge electric force. Note that the electric field
is given in kcal/(mol e Å).
150 kcal_mol/(e Å) ~ 65 V/nm
Assuming your system is ~300 Å in length along the z-axis, you are
applying something like ~2000 V across the membrane.
Sure, electric fields in synthetic nanopores can be extremely high,
but even for these pores, a 1 V potential drop transverse to the
membrane is considered big. It suffices to say that a membrane with
nanoscale thickness would not be stable with such a voltage across it.
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
On Tue, Jan 27, 2015 at 11:26 AM, Dawid das <addiw7_at_googlemail.com> wrote:
> Dear NAMD experts,
>
> I want to simulate permeation of protein through silicon nitride nanopore.
> I have equilibrated the system, everything was fine till I turned the field
> on.
> After ca. 60 steps of simulation I get an error:
>
> ERROR: Atom 51623 velocity is 70243.6 -303988 291675 (limit is 12000, atom
> 390 of 1094 on patch 28 pe 0)
> ERROR: Atom 86282 velocity is -998068 4.2818e+06 -4.08232e+06 (limit is
> 12000, atom 674 of 1094 on patch 28 pe 0)
> ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
> patch 28 pe 0).
> ERROR: Exiting prematurely; see error messages above.
>
> I have done succesfully similar simulation for DNA permeation. Could you
> give me a tip
> where I should look for an error?
> This is my input file:
>
> # NAMD config file
> numsteps 7500000
> structure pore+protein_all.psf
> coordinates pore+protein_all.pdb
> outputName run0
> XSTfile run0.xst
>
> bincoordinates eq3.coor
> binvelocities eq3.vel
> extendedSystem eq3.xsc
>
> langevin on
> langevinDamping 20
> langevinTemp 295
> langevinHydrogen off
>
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 14
> margin 3
>
> binaryOutput yes
> binaryRestart yes
>
> parameters par_all27_prot_na.prm
> parameters par_silicon_ions_NEW5.inp
> paraTypeCharmm on
> wrapAll yes
> wrapNearest yes
> COMmotion no
>
> outputEnergies 1
> outputTiming 1
> xstFreq 1
> dcdFreq 1
> restartFreq 1
>
> timestep 1
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
>
> Pme on
> PmeGridSizeX 96
> PmeGridSizeY 96
> PmeGridSizeZ 288
>
> exclude scaled1-4
> 1-4scaling 1
>
> constraints on
> consKCol B
> consref siliconRest_50.0.pdb
> consKFile siliconRest_50.0.pdb
>
> ## electric field
> eFieldOn on
> eField 0.0 0.0 150.0
>
> The constraint constant I use is 50 kcal/mol.
>
> Best wishes,
>
> Dawid Grabarek
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