[gmx-users] protein-SWCNT md simulation

[Justin Lemkul]

On 1/26/13 4:23 AM, Atila Petrosian wrote:
> Dear all
>
> I want to simulate protein-SWCNT by gromacs. IFf there is a complete
> tutorial about that, please introduce me. According to the Andrea Minoia's
> tutorial, there is no problem for MD simulation of the CNT solitude. I have
> many question about simulation of the protein-SWCNT complex in water.
>
> 1) In tutorial, Andrea Minoia mention only  to the building CNT+ polymer
> solvated system and Andrea Minoia did not mention to the force field.
>

If the tutorial you're referring to is http://chembytes.wikidot.com/grocnt, then 
it is stated that the force field is OPLS-AA.

> 2) If I use a specific force field for protein to obtain top file (pdb2gmx)
> and If I use g-x2top to obtain top file for SWCNT, how to do simulation
> this complex system?
>

You would create a topology that includes a topology for both.  Since both 
pdb2gmx and g_x2top write topologies as .top, you would have to make very simple 
adjustments to one or both of them to become .itp files to be #included in a 
master system .top file.  See here:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

Once you have that, you can #include them however you like, CNT .itp within 
protein .top, or vice versa, or #include both as .itp files within a new .top of 
your own creation.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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