[gmx-users] Nucleic acid simulation

Thomas Schlesier schlesi at uni-mainz.de
Wed Jul 4 17:14:59 CEST 2012

Heard that RNA/DNA system could be a little trickier than proteins due 
to the many negative charges.

I found somewhen a nice article about RNA simulations in general. 
Probably some questions you have / will have are answered there:

A short guide for molecular dynamics simulations of RNA systems
Yaser Hashem, Pascal Auffinger
Methods 47 (2009) 187–197


Am 04.07.2012 16:52, schrieb gmx-users-request at gromacs.org:
> On 7/4/12 6:45 AM, Ravi Raja Merugu wrote:
>> >  Hello every one,
>> >
>> >  Im interesting in performing a MD for Protein - RNA complex , Can any
>> >  one suggest a good  tutorial.
>> >
> Such systems do not differ significantly from simulations of simple proteins in
> water, since pdb2gmx can produce topologies for both proteins and nucleic acids.
>    The remaining workflow is basically the same.
> -Justin

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