From: lcbllcc_at_gmail.com
Date: Thu Sep 26 2013 - 04:07:26 CDT
Hi all,
if you are interested, we have GolP ( Gold parameter + OPLS/AA
parmetrized by Corni and Iori) in CHARMM format, which can be used with
NAMD.
Golp FF: is an atomistic FF to model Gold Surface and protein
(OPLS/AA) ; image effect ("metal polarization") is also included.
Best,
Luca
> Hi Eddie,
>
> You might want to look at these two approaches to model gold, both of
> which are classical and should work with NAMD. In the first approach
> (see papers by Ana Vila Verde and Janna Maranas,
> http://pubs.acs.org/doi/abs/10.1021/bm9002464 and
> http://dx.doi.org/10.1021/la104814z) the gold model is a simple LJ
> potential; this approach, while simplistic, works well if you are
> interested in a system with many charges (like, say, water+ions+proteins
> adsorbing on gold) because the image charge interactions largely cancel
> out. If you choose to go this way, I have a script to produce a psf
> file for gold that would be a useful starting point for you. The script
> is clunky, though, so you might be better off using the topotools tool
> like Axel said...
>
> The second approach involves a classical representation of gold
> polarizability (see papers by Stefano Corni and E. Iori,
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.21165/abstract and
> http://pubs.acs.org/doi/abs/10.1021/la904765u). You can try emailing
> the authors to see if they have any files/scripts to run simulations in
> NAMD before you start reinventing wheels in this case. I met some of
> the authors and they are very approachable.
>
> I hope this helps. Best,
>
> Ana
>
>
>
>
> On 9/25/13 7:37 PM, Axel Kohlmeyer wrote:
> > On Wed, Sep 25, 2013 at 6:52 PM, Dr. Eddie <eackad_at_gmail.com> wrote:
> >> I thought the protein would be the hard part...
> >>
> >> In the end I would like to look at effect the nanoparticles have on ordering
> >> the system. Thus, to the best I can see right now, I would want the
> >> course-grain model to include a local and global approximation to the
> >> nanoparticle's electric field and surface polarizability due to water and
> >> the proteins. I only expect the gold nanoparticle to interact via high order
> >> electric moments, that depend on its shape, with the proteins. Is that way
> >> off the mark?
> > i don't know. i am not an expert in that field. it looks to me like a
> > multi-scale problem, where you need more than just one kind of
> > calculation, but need to build a coarser scale model based on the
> > previous level and - if available - validate it with suitable
> > experimental data. you mention polarization, but i would expect that
> > this would be mostly determined by the surrounding solvation shell and
> > attached molecules, so there is a good chance that this could be very
> > well approximated with a non-polarizable all-atom model. there is the
> > group of gary grest at sandia that does pretty big simulations related
> > to that. perhaps, there is something you can learn from their
> > publications.
> >
> > not sure how you can coarse grain this efficiently. and specifically
> > include electrostatics well enough. it is possible to fit a multi-pole
> > expansion to a set of point charges.
> >
> > at the higher level, you probably need something that is purely shape
> > based and has an efficient to compute solvent. martini style coarse
> > graining may be not enough for a reasonably large system, but could be
> > used at an intermediate step.
> >
> > at the high level, it looks like you want to use something that models
> > particles purely based on shape, but with a choice of shape variation.
> > that would require either an implicit solvent via brownian dynamics or
> > you could look at stochastic rotation dynamics (SRD). the group of
> > sharon glotzer does work on "shaped nanoparticles", so perhaps you can
> > steal some good ideas from them.
> >
> > there are likely many more people working on aspects of these kind of
> > systems. i doubt that you will get something useful by just setting up
> > a system with "some model" and let it go. this rarely works. MD
> > simulations almost always need "a plan(tm)".
> >
> > axel.
> >
> >> In the end I will be trying to replicate a colleagues experimental results
> >> of order inducement as a function of gold nanopartcile concentration and
> >> other measures.
> >>
> >> Thanks again!
> >> Eddie
> >>
> >>
> >> On Wed, Sep 25, 2013 at 11:34 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >>> On Wed, Sep 25, 2013 at 6:25 PM, Dr. Eddie <eackad_at_gmail.com> wrote:
> >>>> Hi all,
> >>>> I would like to use namd to perform a simulation with coarse-grain
> >>>> proteins
> >>>> around gold nanoparticles. I see vmd has a coarse grain model builder so
> >>>> that leaves the gold nanopartciles. Are there any tools for building
> >>>> these
> >>>> nanoparticles and generating their psf using the charmm forcefield? I
> >>> do you have an idea how you want to model / coarse grain the gold
> >>> atoms? and how the interaction between the proteins and the gold
> >>> particle? just having a tool to build the coarse grain model for the
> >>> proteins, is the least of your problems.
> >>>
> >>> building custom psf files from scripting can be done with the topotools
> >>> plugin.
> >>>
> >>> axel.
> >>>
> >>>> thought I'd ask before reinventing the wheel so to speak.
> >>>> Thanks!
> >>>> Eddie
> >>>
> >>>
> >>> --
> >>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >>> International Centre for Theoretical Physics, Trieste. Italy.
> >>
> >>
> >>
> >> --
> >> Eddie
> >
> >
>
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