# Help with setting up topology for supramolecular polymers **URL:** \ **Category:** User discussions\ **Created:** [December 13, 2024, 1:44pm UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807 "2024-12-13T13:44:52Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Berith](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Berith](https://gromacs.bioexcel.eu/u/Berith)\ **Post date:** [December 13, 2024, 1:44pm UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/1 "2024-12-13T13:44:52Z")
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 ---
**Author:** ![pkfaustino](https://avatars.discourse-cdn.com/v4/letter/p/43a26b/32.png) [@pkfaustino](https://gromacs.bioexcel.eu/u/pkfaustino)\ **Post date:** [December 14, 2024, 2:33am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/2 "2024-12-14T02:33:10Z")
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. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 10:21am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/3 "2024-12-16T10:21:31Z")
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. ---
**Author:** ![Berith](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Berith](https://gromacs.bioexcel.eu/u/Berith)\ **Post date:** [December 16, 2024, 10:33am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/4 "2024-12-16T10:33:18Z")
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? ---
**Author:** ![Berith](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Berith](https://gromacs.bioexcel.eu/u/Berith)\ **Post date:** [December 16, 2024, 10:36am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/5 "2024-12-16T10:36:14Z")
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? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 10:47am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/6 "2024-12-16T10:47:51Z")
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? ---
**Author:** ![Berith](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Berith](https://gromacs.bioexcel.eu/u/Berith)\ **Post date:** [December 16, 2024, 11:01am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/7 "2024-12-16T11:01:55Z")
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. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 11:07am UTC](https://gromacs.bioexcel.eu/t/help-with-setting-up-topology-for-supramolecular-polymers/10807/8 "2024-12-16T11:07:00Z")
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.