[gmx-users] DNA podophyllotoxin

[Justin A. Lemkul]

Hovakim Grabski wrote:
> Dear Gromacs users,
> I set up a simulation between the  DNA fragment and 6 podophyllotoxin 
> molecules,  the topology files were generated with acpype,  simulation time
> was 2.8 nanoseconds, but the results are not what I expected. 4

What were you expecting?  Simulations are often surprising ;)  Also realize that 
2.8 ns is an extremely short simulation.  I'm not suggesting that you 
necessarily blindly run several hundred ns, but time frame may be an important 
consideration.

> molecules of PTOX formed an aggregate and then formed hydrogen bonds 
> with the end of the DNA molecule. Could this happen because of the 
> topology file?

Almost certainly, but that's true of everything in a simulation.  The force 
field (and thus the topology, which is part of the force field) governs 
everything in the simulation.

-Justin

-- 
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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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