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I want to run MD simulations of a polymer, but I want to start from different physical conformations. My question is, how do I obtain these conformations? Is there a software which performs this?

Let's say I want to run a MD simulation for a polymer in an "extended" state and from a "collapsed" state. I obtain PDBs from CHARMM, but they are always in the extended state. How do I cleanly obtain a collapsed state, using something like Rotational Isomeric State model, or something along those lines.

Any advice you have would be appreciated!

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    $\begingroup$ RDkit, openbabel, CREST can all generate ensembles of conformations of a molecule. I am not sure how to ask specifically for extended and collapsed, but it is quite simple to get a bunch of "random" structures of the same molecules, and even rank them from most to least favorable (in a vacuum or simple continuum). Polymers quickly get out of hand though, they are so floppy, for C10 and bigger, I wouldn't want to generate every possible conformer, it would take too long $\endgroup$
    – B. Kelly
    Jul 28, 2022 at 13:21
  • $\begingroup$ spartan can also do this $\endgroup$
    – B. Kelly
    Jul 31, 2022 at 23:13

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You could try to run a GROMACS simulation with COLVARS, which takes the radius of gyration as a possible collective variable. Running an umbrella sampling simulation with a suitable set of weights should give you an ensemble of snapshots with the desired distribution of radii of gyration.

Alternatively, you could run an MD simulation but with every particle of the polymer harmonically tethered (with a very weak force constant!) to the simulation cell origin. Making the force constant larger or smaller would then make the average radius of gyration smaller or larger.

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  • $\begingroup$ I gave my +1 long ago (and very enthusiastically). Congratulations on answering two of these questions. Do you think you can browse through that list and answer some more?! $\endgroup$
    – Nike Dattani
    Nov 1, 2022 at 20:19

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