Re: Gold nanoparticle

From: Luca Bellucci (lcbllcc_at_gmail.com)
Date: Fri Sep 27 2013 - 03:10:09 CDT

Hi Eddie,
you can find a version of GolP here:

http://web.fisica.unimo.it/prosurf/download/download.php

It is worth noting that GOLP describe the interaction betwenn biomolecules
(OPLS) and gold SURFACE and NOT Naoparticles. It is defined with the same
potential-energy functions of the OPLS FF, therefore it is compatible with
bio-oriented MD codes and it includes a polarization effect due to
image charges induced by the adsorbed charge.

CHARMM formatof GOLP for NAMD is not present for the download,
however, I can send topology, parameters and tutorial privately.

Luca
 
> 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

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