Gromacs

Polymers

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    GROMACS is well-suited for running simulations of polymeric materials.  One of the questions frequently asked on the gmx-users list is how to create a topology for a polymer containing many repeat units.  Probably the simplest way is to create .rtp entries for the desired force field, and use pdb2gmx to create the topology.  To do so requires (at least) three types of residues to be defined:

    1. A "starting" residue, defining the "beginning" of the chain
    2. The repeat (internal) residues
    3. An "ending" residue, defining the "end" of the chain

    An example of how to implement such entries can be found here, for the case of polyethylene under the OPLS-AA force field.

    There is also an online server that allows the user to build certain types of polymers, which does not solve the issue of building the topology, but can certainly be useful in generating the initial coordinates for the material.

    Page last modified 23:14, 17 Mar 2014 by JLemkul?