Well, the end caps contain a few pentagons so the angle terms for those atoms would have to change from the normal 120 degrees used for hexagons. Other than that, I don't think the force field parameters would have to change. What do you mean by the tube "breaking apart"? That sounds like you don't have the right connectivity in your topology file. Bob
On Fri, May 9, 2008 at 11:21 AM, Christopher Stiles <[EMAIL PROTECTED]> wrote: > I am attempting to run a simulation involving a (10,10) CNT that is capped > on one side. Each time I do this the tube breaks apart in the first few > steps, so I am thinking that the force fields must be modified from how I > have them set just for an un-capped CNT. If any one has done this or could > point me in the correct direction I would be very grateful. > > > > I have also included a copy of my *.pdb file in case that is the issue. > > > > Thank you! > > ~Christopher Stiles > > > > P.S. I use the following modifications to the ffgmxbon.itp file: > > > > ##################################### > [ bondtypes ] > ; i j func b0 kb > C C 1 0.14210 478900. > ##################################### > [ angletypes ] > ; i j k func th0 cth > C C C 1 120.000 397.480 > ##################################### > [ dihedraltypes ] > ; i l func q0 cq > C C 1 0.000 167.360 > ##################################### > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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