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
[gmx-users] SD integrator
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
Fwd: [gmx-users] SD integrator
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
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
[gmx-users] sd integrator
Hi, The sd integrator is described in the manual as follows: sd An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. With constraints, coordinates needs to be constrained twice per integration step. Depending on the computational cost of the force calculation, this can take a significant part of the simulation time. The temperature for one or more groups of atoms (tc_grps) is set with ref_t [K], the inverse friction constant for each group is set with tau_t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld_seed. When used as a thermostat, an appropriate value for tau_t is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau_t. It is not clear what is the purpose of this integrator and how is it different from ld. Can someone refer me to a paper? Can such an integrator help in making trajectories less deterministic? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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: [gmx-users] sd integrator
On 22/09/2011 6:21 AM, Sai Pooja wrote: Hi, The sd integrator is described in the manual as follows: sd An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. With constraints, coordinates needs to be constrained twice per integration step. Depending on the computational cost of the force calculation, this can take a significant part of the simulation time. The temperature for one or more groups of atoms (tc_grps) is set with ref_t [K], the inverse friction constant for each group is set with tau_t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld_seed. When used as a thermostat, an appropriate value for tau_t is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau_t. It is not clear what is the purpose of this integrator and how is it different from ld. Can someone refer me to a paper? See manual section 3.8 and ref therein. Can such an integrator help in making trajectories less deterministic? It's still going to be deterministic, because the RNG is. Mark -- 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: [gmx-users] sd integrator
But is the effect of varying ld_seed.. can that make different trajectories stochastic? On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 22/09/2011 6:21 AM, Sai Pooja wrote: Hi, The sd integrator is described in the manual as follows: sd An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. With constraints, coordinates needs to be constrained twice per integration step. Depending on the computational cost of the force calculation, this can take a significant part of the simulation time. The temperature for one or more groups of atoms (tc_grps) is set with ref_t [K], the inverse friction constant for each group is set with tau_t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld_seed. When used as a thermostat, an appropriate value for tau_t is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau_t. It is not clear what is the purpose of this integrator and how is it different from ld. Can someone refer me to a paper? See manual section 3.8 and ref therein. Can such an integrator help in making trajectories less deterministic? It's still going to be deterministic, because the RNG is. Mark -- 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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: [gmx-users] sd integrator
On 22/09/2011 9:57 AM, Sai Pooja wrote: But is the effect of varying ld_seed.. can that make different trajectories stochastic? Any single MD or SD trajectory is literally stochastic. Either can start from the same point with respectively different ld_seed or gen_seed and diverge. Mark On Wed, Sep 21, 2011 at 7:40 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 22/09/2011 6:21 AM, Sai Pooja wrote: Hi, The sd integrator is described in the manual as follows: sd An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. With constraints, coordinates needs to be constrained twice per integration step. Depending on the computational cost of the force calculation, this can take a significant part of the simulation time. The temperature for one or more groups of atoms (tc_grps) is set with ref_t [K], the inverse friction constant for each group is set with tau_t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld_seed. When used as a thermostat, an appropriate value for tau_t is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau_t. It is not clear what is the purpose of this integrator and how is it different from ld. Can someone refer me to a paper? See manual section 3.8 and ref therein. Can such an integrator help in making trajectories less deterministic? It's still going to be deterministic, because the RNG is. Mark -- 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
