Re: Fwd: [gmx-users] SD integrator
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: Fwd: [gmx-users] SD integrator
Are you sure that the source of instability is the CNT, not the protein? If yes, what makes you to think so? If you freeze all the atoms of the CNT, does it work well? Dr. Vitaly V. Chaban On Sun, Sep 15, 2013 at 11:07 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: 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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: Fwd: [gmx-users] SD integrator
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 listgmx-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 listgmx-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 listgmx-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
