[gmx-users] polymer-topology generation
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
> 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
> 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
> 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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Justin A. Lemkul, Ph.D.
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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