How to define the volume of the simulation space?

[Ljiljana Stojanovic]

Hi,

I am trying to simulate the system of several polymer chains in the confined space. I am planning to use NVT (canonical) ensemble with Nose-Hoover thermostat. Could someone, please, answer me is NVT ensemble available in Simbody/Molmodel and is it possible to define the volume and the shape of the simulation space?

Thanks for the help.

Best regards,
Ljiljana

[Michael Sherman]

Hi, Ljiljana.

If by NVT you mean an explicit solvent simulation, I don't think it makes sense to use Molmodel for that. It is only suited for simulation in implicit solvent, in which case the volume is undefined (or infinite).

If you want to use more conventional MD, I would highly recommend using OpenMM instead: https://simtk.org/home/openmm.

Regards,
Sherm

[Ljiljana Stojanovic]

Thank you very much for such a quick response!
I wanted to perform simulations in vacuum, but I didn't know if it was possible in Molmodel. Thank you for suggestion to use OpenMM, haven't considered that option. I noticed that it is suitable for my simulations.

Thank you once again.

[Michael Sherman]

Molmodel can be used in vacuum or implicit solvent, just not explicit solvent.

Sherm

[Ljiljana Stojanovic]

Ok. Thanks once again.
Regards,Ljiljana