Hi all,
I am new to GROMACS and going to use it for simulating supramolecular structures. However, I don’t know how to generate the topology for this. I already have the relaxed structure of the BTA monomer, but now I would like to assemble it as a supramolecular polymer and simulate this. Nevertheless, as I said, I’m not sure how to do this.
I hope someone can help me / give me tips on how to proceed!
Thank you,
Berith
Hi.
First, choose the ideal force field to use. Have you already chosen your force field?
Then, you can use any software, e.g. Avogrado, to write your molecule and then generate the topology, according to the force field used.
I also recommend using the SMILES Chemistry form to make it easier.
Best regards.
What do you mean with “supramolecular”?
The easiest way is to make an rtp file with the monomer. Then pdb2gmx can generate the topology for the polymer. You would like need special entries for the two ends.
Hi,
Thank you for your response.
With “supramolecular” I mean monomers who are not covalently bonded to each other, but bonded through intermolecular interactions.
How does pdb2gmx generate the topology for the polymer? Can one specify the number of monomers wanted in the file?
What kind of entries do I need for the two ends?
Hi,
Thank you for your response!
Yes, I know which force field I would like to use. In Avogrado I can write multiple units of monomers?
I still don’t understand. Do you want to connect monomers through intermolecular-interactions? Or do you already have polymers and you want to connect different polymers with bonds?
Hi, ah sorry, my bad. My goal is currently to simulate a stack of 48 units of the same monomer, and see for example which interactions are important for a stable fiber. I do not know how to pre-stack my monomers and from there make the topology.
I don’t understand what you mean with “a stack”. But if you need to connect monomers into a polymer, the rtp file mechanism is very convenient. This is used for proteins, which are also polymers.