[gmx-users] Atomistic Simulation

Hardy, Adam ah259 at hw.ac.uk
Tue Dec 3 12:17:58 CET 2013

I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far.

I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder.

There may well be other ways to do this but I haven't found them yet.

On 3 Dec 2013 10:14, panzu <sergio.panzuela at estudiante.uam.es> wrote:
  Hello to everybody,

I am new in atomistic simulations and a have some doubts about how to do it.

I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane.
My  questions are, ¿Where do I get the pdb files of these molecules
from? and ¿How do I know which force field I should choose in pdb2gmx
in order to make the itp file?

Thanks in advance,


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