[gmx-users] polymer-topology generation

Justin Lemkul jalemkul at vt.edu
Mon Dec 23 22:46:02 CET 2013



On Mon, Dec 23, 2013 at 4:33 PM, decaiyu <dyu at dow.com> wrote:

> 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
> material.
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/polymer-topology-generation-tp4442044p5013493.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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