Re: [gmx-users] Membrane Equilibration
what happens to your energy before the observed crash? does the crash happen at the same time-step each time? Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 5:22 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman coupling. However, I read that Parinello-Rahman is not great for equilibration so I thought I would do a small run using the Berendsen barostat to decrease the chances of large oscillations. I then used the .gro file obtained from that run to start a new run using Parrinello-Rahman. I am not sure if that's the correct way to go about doing what I want to do. My Parrinello run also terminated a little while in, with the error that 2 of my atoms have moved further apart than the cut-off distance. A part of my mdp file is pasted below and I was wondering if anyone had any suggestions as to stop that from happening. My time step is 0.02 ps and I thought increasing tau-p might work. I am using the compressibility from the map file on the Martini website and am worried that might be too large. Any help will be super useful! Let me know if you need any more information. ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = nose-hoover ; Groups to couple separately = tc-grps = DPPC W ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 1.0 ref_t= 320 320 nsttcouple = 1 ; Pressure coupling = Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 0.0 0.0 nstpcouple = 5 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 105 gen_seed = 473529 -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: [gmx-users] Membrane Equilibration
ref_p= 0.0 0.0 ?? Are you sure about this?? On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: what happens to your energy before the observed crash? does the crash happen at the same time-step each time? Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 5:22 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman coupling. However, I read that Parinello-Rahman is not great for equilibration so I thought I would do a small run using the Berendsen barostat to decrease the chances of large oscillations. I then used the .gro file obtained from that run to start a new run using Parrinello-Rahman. I am not sure if that's the correct way to go about doing what I want to do. My Parrinello run also terminated a little while in, with the error that 2 of my atoms have moved further apart than the cut-off distance. A part of my mdp file is pasted below and I was wondering if anyone had any suggestions as to stop that from happening. My time step is 0.02 ps and I thought increasing tau-p might work. I am using the compressibility from the map file on the Martini website and am worried that might be too large. Any help will be super useful! Let me know if you need any more information. ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = nose-hoover ; Groups to couple separately = tc-grps = DPPC W ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 1.0 ref_t= 320 320 nsttcouple = 1 ; Pressure coupling = Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 0.0 0.0 nstpcouple = 5 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 105 gen_seed = 473529 -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: [gmx-users] Membrane Equilibration
On 6/11/13 1:13 PM, HANNIBAL LECTER wrote: ref_p= 0.0 0.0 ?? Are you sure about this?? That's a likely culprit. See below for another. On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: what happens to your energy before the observed crash? does the crash happen at the same time-step each time? Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 5:22 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman coupling. However, I read that Parinello-Rahman is not great for equilibration so I thought I would do a small run using the Berendsen barostat to decrease the chances of large oscillations. I then used the .gro file obtained from that run to start a new run using Parrinello-Rahman. I am not sure if that's the correct way to go about doing what I want to do. My Parrinello run also terminated a little while in, with the error that 2 of my atoms have moved further apart than the cut-off distance. A part of my mdp file is pasted below and I was wondering if anyone had any suggestions as to stop that from happening. My time step is 0.02 ps and I thought increasing tau-p might work. I am using the compressibility from the map file on the Martini website and am worried that might be too large. Any help will be super useful! Let me know if you need any more information. ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = nose-hoover ; Groups to couple separately = tc-grps = DPPC W ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 1.0 ref_t= 320 320 nsttcouple = 1 ; Pressure coupling = Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 0.0 0.0 nstpcouple = 5 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 105 Here is another issue. You're re-generating velocities (destroying the previous equilibration) with a barostat that doesn't usually play nice under such circumstances, and you're generating velocities for a temperature well below the target defined in ref_t. That can cause the thermostat to go haywire, which then has negative effects on the pressure (which comes from kinetic energy and the virial), which can lead to collapse. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
