Ok. Thanks once again.
Regards,Ljiljana

Thank you very much for the answer. Yes, I wanted to use the internal coordinates to constraint bond lengths and angles, that was the only reason. However, the user's guide states that it is only possible to use constraints for angles which involve H atoms. Is there maybe any way to constraint all b...

Dear all, I've been trying to simulate a system of polymer chains in vacuum using internal variables. The plan is to constraint all bond lengths and angles, and to vary only several torsional angles. I've been trying to use Molmodel with SImbody for this purpose, because SImbody has Internal variabl...

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.

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 t...

Well, the backbone does not resemble any of the amino acids. It is composed of two benzene rings with backbone aliphatic chains, tiophene ring, etc. I think maybe it would be possible to hack the Protein.h, and to define the structure of my monomer instead of some of the amino acids. I will probably...

I would like to determine the structure of one organic polymer chain (not biopolymer) using internal variable approach implemented in Simbody. The monomer of the studied polymer has complicated structure, it is composed of several rings, and I would like to treat the rings as rigid bodies and to fre...

Oh wait did you mean non-biological polymers? For that you would need to write your own little program using molmodel, or hack the MMB source. I have an object called spRNA that might serve as an example. Thank you very much for the answer, Sam . I intend to use internal variables and to simulate n...

Dear all, Could you, please, answer me whether it is possible to use Molmodel/Simbody for MD simulation of polymers? Do you have any suggestion how ti define its initial structure? Is it possible to define somewhere the structure of a monomer unit, and then to use it to construct polymer, as it is u...