https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
-Justin On Mon, Dec 23, 2013 at 4:33 PM, decaiyu <d...@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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- ========================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
