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!