----- Original Message ----- From: Tree <[email protected]> Date: Sunday, March 8, 2009 6:35 Subject: Re: [gmx-users] Polymer entanglement simulation To: [email protected], Discussion list for GROMACS users <[email protected]>
> Dear Justin and Users: > > Thank you for your fast reply.> > First, I want to clarify the "entanglement", so I can get more accurate > consult from you! :) > > Of course, the non-bonded interaction makes entanglement "among" polymer > chains.> > However, "Entanglement" here means the "intra"chain (intramolecular) one. > In other words, one chain polymer (having enough monomers inside, e.g. 1 > chain polymer containing 20 monomers) can be entangled with itself. > This is > the reason that I gave force filed parameters related to the bond (stretch), > angle, dihedral, and improper dihedral. I don't understand what you mean by "entanglement", nor what this has to do with your force field parameters. > This is also reason that I have suspected the topology file, which assign > force field...> > In addition, I am putting my setting here.> > tc-grps = carbon hydrogen This is a train wreck waiting to happen. Please consider doing some more background reading and/or tutorial material :-) Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
