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