VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Feb 01 2016 - 05:30:30 CST

>
> 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.

It would be perhaps easier if you create a unit of your larger system say
"small bead-X" which interacts with other "small bead-Xs" and some solvent
molecules. Many "small bead-X" would come together to make the giant
sphere. You could start them off in a sphere's shape so you don't have to
wait for them to assemble. This would also help you resolve the potential
between the surface of the sphere and whatever it is interacting with.
Moreover going with a "small bead-X" would also help with size
consistencies across 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.

The exact answer to your question can only be given by you. This is because
the level of coarse-graining depends on you.
Mass/Charge -- how bonds are going to be handled etc are decisions you need
to make to define your system. Past that point what I can tell you (not
sure if you already know this --??)

To simulate a system in any engine you need a definition of your system in
the form of a PDB file. This file explicitly holds coordinates of atoms
which define your system. Coupled with this is a file which holds
information on mass, charges, bonds etc. This is would become to long for a
simple post if I continue - so I would say that you should read some intro
text on Computational Chemistry and on simulating biological system. Some
text on coarse-graining would also be helpful.

After that define your system. This is what the literature on
coarse-graining will help you with.

Once that is done - assuming you end up using NAMD with CHARMM style
parameter set you would need to have a PDB file holding your system and a
PSF which will hold all the other information necessary to evaluate the
dynamics of your system. See the structure of the PSF. It has sections
defining what parts of your system are subject to what aspect of the
function. What will go into those sections will depend on what sort of a
system you end up having. Follow a tutorial to build a simple protein's PSF
file to see what happens.

Hope this was helpful.

On Mon, Feb 1, 2016 at 11:32 PM, Shubham Mishra <shubham.root_at_gmail.com>
wrote:

> 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
> replies.
>
> 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
> begin with.
>
> 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.
>
> Regards,
> Shubham Mishra
> --
> B.E.(Hons.) Chemical Engineering
> Birla Institute of Technology & Science, Pilani - Hyderabad Campus
> India
> 

-- 
Best,
/A