[gmx-users] polymer-topology generation

decaiyu dyu at dow.com
Mon Dec 23 22:34:36 CET 2013

Dear All,Can anyone help me find the link to the example to make polymer
residue files?The link below does not work on the website.Best Regards,Decai
Yu  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

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