From: Dr. Eddie (eackad_at_gmail.com)
Date: Thu Sep 26 2013 - 09:42:36 CDT
Thank you all so much for your help!!! I really appreciate the references,
suggestions, clarifications and offers. It sounds like GoIP will do what
I'd like to try and I think that will let me create and model the system I
have in mind. Please let me know how I can obtain GoIP.
Thanks again for all your help!
Eddie
On Thu, Sep 26, 2013 at 4:07 AM, lcbllcc_at_gmail.com <lcbllcc_at_gmail.com>wrote:
>
> 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
> > >
> > >
> >
>
>
>
-- Eddie
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