Thanks. From your publications it seems that you have been simulating with infinite CNTs. I am trying to use finite CNTs and I am generating my topology files according to
http://chembytes.wikidot.com/grocnt. I am modeling the peripheral Carbon atoms with two bonds by specifying it in the atomname2type.n2t file. I am still not sure as to what is the source of this discrepancy. After a few tests I think this can be caused by improper parameterization of the bonds but I am not sure how to go about correcting any discrepancies. On Fri, Sep 13, 2013 at 5:53 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > Do you couple CNT as a separate T-group? It should be done so. > > I think your systems blows up because of incorrectly defined bonded > parameters for the tube, not due to thermostatting. For instance, you might > not define all the valence angles and dihedrals. > > See my papers for the parameters for CNT, if you need such... > > > Dr. Vitaly V. Chaban > > > On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER < > hanniballecte...@gmail.com > > wrote: > > > However, even if position restraints are not used, the error can be > > reproduced. I am constraining the bonds in my CNTs though. > > > > I was wondering if you could point me to some parameters for CNT. > > > > > > On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER < > > hanniballecte...@gmail.com> wrote: > > > >> I am position restraining the CNT group. That affects the degrees of > >> freedom. > >> On Sep 13, 2013 1:43 PM, "Dr. Vitaly Chaban" <vvcha...@gmail.com> > wrote: > >> > >>> There must be some problem with degrees of freedom in your system... > >>> > >>> > >>> Dr. Vitaly V. Chaban > >>> > >>> > >>> ---------- Forwarded message ---------- > >>> From: HANNIBAL LECTER <hanniballecte...@gmail.com> > >>> Date: Fri, Sep 13, 2013 at 7:15 PM > >>> Subject: [gmx-users] SD integrator > >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >>> > >>> > >>> Hi all, > >>> > >>> I have been posting for a while with my problems in simulating peptides > >>> inside CNTs. After a lot of trials it seems like simulating the CNT > with > >>> bonds and angles seems like a wise thing to do. > >>> > >>> I am using the SD integrator + PR barostat. It seems like improper > >>> thermostatting can blow up the system. For example, when I am trying to > >>> simulate with tau-t for CNT as 1.0 the system blows up for 300K. The > >>> output > >>> temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K. > >>> > >>> However, if a stronger coupling is used tau-t = 0.005, the system > works > >>> fine. Are there any artifacts for coupling the CNT group with such a > low > >>> tau-t? > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists