[gmx-users] DNA podophyllotoxin

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 30 18:15:24 CEST 2012

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 

> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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