From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Jan 27 2015 - 14:04:26 CST
I wrote the NAMD Bionanotechnology Tutorial, so the confusion is my
fault. Sorry about that. I chose a very large electric field so that
you could see the DNA translocation in several minutes of simulation
(using a typical workstation in 2007). It's probably pushing the
limits of what can be done with stable dynamics. You can probably
reduce by a factor of 5 or 10 and still see DNA translocation fairlly
quickly with a modern workstation.
Since these were rather extreme conditions, the tutorial includes a
much longer trajectory at 6 V (still high) so that you can analyze it.
In any case, for comparison to experiments, you'll probably want more
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
> Dear Jeff,
> Well I thought of the same thing, that this is way too big.
> But this was suggested by NAMD Bionanotechnology tutorial.
> Anyway what I want to get is 6 V and it was saying so in the tutroail that 6V corresponds to 150 > kcal.(mol A e) of electric field.
> I did my own calculations obviously and according to them this electric field should be much lower > than 150 kcal/(mol A e).
> So I will try with what I get ;).
> Thank you for reply,
On Tue, Jan 27, 2015 at 1:22 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> 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.
> 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
>> 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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