Polymer simulation

[Ljiljana Stojanovic]

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 used in the case of proteins?
Thank you in advance.

Best wishes
Ljiljana

[Samuel Flores]

Hi Liljana,

If you're looking to use internal coordinates, my guess is that it's not straight-up MD that you want to do. Internal coordinates lets you control the flexibility, and apply forces and constraints in ways MD may not. Perhaps that's what you're after?

In any case I wrote MMB to do this sort of thing. You can download the executables and read the tutorial guide, other than that I will be happy to answer any questions you may have about how to use it. If the tutorial doesn't have an example of what you're after you can tell me what you're trying to do, there is probably some way to do it in MMB.

Sam

[Samuel Flores]

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.

[Ljiljana Stojanovic]

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 nonbiological polymer. Could you answer me, please, where can I find program spRNA which could be an example. Thanks once again.
Ljiljana

[Samuel Flores]

that's not a program, it's just an object within MMB. I was suggesting you hack the MMB source to get it to do what you want.

What is it you want to do? That should be my first question.

Sam

[Ljiljana Stojanovic]

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 freeze all bond lengths and angles, except torsion angles. I will use calculated potential energy curves to extract the parameters for torsional motion.
Ljiljana

[Samuel Flores]

What does the backbone look like? Is it anything like a protein backbone (N, CA, C)?

If I were doing this I would probably try to hack the Protein class to do what you want. But I'm a bit biology-biased. Maybe it's better to start with Compound and make a new daughter class from there.

In any case sounds like MMB is may not be all that useful to you, so there might not be all that much I can do to help.

[Ljiljana Stojanovic]

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 try that way.
Thank you very much for the suggestion and help.
Best regards
Ljiljana