Dear Lammps users,
I want to rum MD simuation of a RNA structure only. I have both amber topology/coords and psf files for my structure. Could any one please guide me how to run simulations ? It would be great if there is any tutorial on RNA/DNA MD simulation so I can learn how to run calculations and analyse results.
thank you
Regards,
Sajid
Dear Lammps users,
I want to rum MD simuation of a RNA structure only. I have both amber
topology/coords and psf files for my structure. Could any one please guide
me how to run simulations ?
that would be primarily the task of your adviser. there is a tool to
convert amber input to LAMMPS, but it has long been unmaintained and
thus it will most likely not work and is definitely not ready for a
beginner.
It would be great if there is any tutorial on
RNA/DNA MD simulation so I can learn how to run calculations and analyse
results.
running MD for RNA/DNA is in principle not different from running MD
for any other kind of system. there may be a few specific quirks, e.g.
how to handle counter ions.
again, the first part is the job of your adviser or somebody that you
may be referred to by your adviser, and yourself. there are text books
and plenty generic MD tutorials around. please note that LAMMPS
provides a "manual", i.e. it is expected that the reader has
familiarized him/herself with MD beforehand. you will not find a
tutorial that has customized step by step instructions specific to
your problem that you can blindly follow. procedures and protocols can
be inferred from the methods description in the literature. there are
likely a large number of publications studying similar systems that
you can use as a reference. in fact, you should start by reproducing
the results from a few of them. while it is fairly easy to get an MD
simulation "running", it can take a significant amount of effort to
reach a point where you can draw meaningful conclusions.
axel.