VMD-L Mailing List
From: Shubham Mishra (shubham.root_at_gmail.com)
Date: Mon Feb 01 2016 - 04:32:50 CST
Thank You Ashar for that extensive insight. That clarified almost
everything I needed for this work.
My apologies for making this thread unstructured by posting individual
One would go about doing what you are doing by first arriving at a force
> field. This is basically what you said about repulsive potentials etc.
> Depending on what plays a role in your system and what doesn't you would
> have to arrive at potentials which would govern the dynamics of your system
Yes, we have decided on the potential that needs to be used here. We just
want to study the non-bonded interactions so van der Waals force and
electrostatic interaction. So Lennard-Jones 12-6 potential is we want to
If you coarse grain everything else accept water - you will hardly see much
> improvement in your computational time. You need to use a coarse grained
> model for water as well to go along with this entire exercise.
That is definitely something I did too wrong. I will work that out now.
You said that you only want a sphere - which is hollow. Hollow doesn't and
> shouldn't mean vacuum -- you would need to define some way in which you
> model the contents of this sphere with a continuum
I don't really want a hollow sphere. I just need sphere, which should have
the mass of the nanoparticle and no other properties of the material that
makes it - which technically is erroneous, but we hope that shall give a
crude idea of how our system behaves - while the surface of the sphere
needs to be modified either by making it patchy or by self-assembling the
capping agents on the sphere surface, which I also hope can be done through
coarse-graining the molecules under study.
If you want just one GIANT sphere - then there is no question of making it
> hollow because you would have to give it a VDW radii and perhaps some other
> potential so that it reproduces some properties of the system you are
> trying to model.
Agreed. I will keep a note of this while creating the system.
All said I am still at loss of not knowing what tools to use to
define/create my system yet. If I could just be told where to start
creating a system as such I guess the extensive tutorials on the web would
help me further.
Thanks again for your time and your answer.
-- B.E.(Hons.) Chemical Engineering Birla Institute of Technology & Science, Pilani - Hyderabad Campus India