From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 25 2013 - 12:37:13 CDT
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
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)".
> 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!
> 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
>> > 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.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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