[gmx-users] What can we do with gromacs?

[Justin A. Lemkul]

mustafa bilsel wrote:
> Hi,
> I would like to ask questions about what we can do with Gromacs.
> 3. For example I have some different molecules and I would like to see 
> their binding affinity to carbon nanotubes. Is it possible to do this 
> simulation with Gromacs? If possible, I should have attractive and 
> repulsive potentials. Which potential(s) in Gromacs should I use for 
> this purpose? 

This question is better posed as a parameterization issue.  I don't know which 
of the force field Gromacs has that would accommodate such a venture, but if 
there is literature precedent, I would start there.  Be advised that 
parameterization is an advanced topic, and you should be prepared to invest more 
time in deriving parameters than in actually collecting data.

http://www.gromacs.org/Documentation/How-tos/Parameterization

> 2. Is it possible to simulate folding mechanism of a protein in closed 
> geometry? closed geometry maybe in cylindrical or cubic shape.

Anything is possible, but the time frame is probably a limiting factor.  Protein 
folding occurs on a time scale that exceeds most simulations.  Small model 
peptides can be done, but even then a significant amount of data needs to be 
collected.  Whether or not you can achieve an exact configuration depends 
entirely upon the quality of the force field model, simulation parameters, and 
extent of sampling.


> 3. Can we check if a protein adhesed or not a to a surface? surface 
> consists of atoms.
> 

Sure.

Gromacs is a very versatile program capable of doing pretty much anything you 
tell it.  Therein lies the problem - whether or not self-consistent force fields 
exist to describe heterogeneous and/or non-biological systems as you've 
described.  Certainly people have worked on such areas, so I would advise you to 
do some extensive background reading and planning.  It will save you a lot of 
time down the road.

-Justin

> 
> Best wishes
> Mustafa Bilsel
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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