[gmx-users] Re: Membrane Equilibration
Hi everybody, It seems that my runs still are crashing. I even decided not to switch over to Parinello-Rahman and continue doing the simulation with a Berendsen barostat and it shuts off after a period of time. I am extremely puzzled as to why this is happening especially since Berendsen is pretty robust. Let me know if you have any further insight! -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038p5009265.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] Re: Membrane Equilibration
Hi everybody, Thank you so much for taking the time to read this. I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface tension. How else could I get a tensionless membrane? As for the generating velocities, I completely forgot that would ruin the equilibrium. Would you recommend saying gen_vel = no or simply raising the gen_temp closer to the required value? If the second how close do you think I should keep it? Sorry for bombarding you guys with so many questions! Also no one has commented on this so I'm guessing using the structure file from the Berendsen run is an okay way to do what I want? Again thanks for the help! Justin Lemkul wrote 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 5:22 PM, Neha lt; nshafique@ gt; 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 list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038p5009046.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] Re: Membrane Equilibration
Exactly so. I think Gromacs issues a warning when you try to initialize velocities with Parrinello-Rahman barostat. But if you performed your equilibration at 105K using Berendsen barostat, I think it should be okay and you should put gen-vel = no. -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038p5009047.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
Re: [gmx-users] Re: Membrane Equilibration
On 6/11/13 1:25 PM, Neha wrote: Hi everybody, Thank you so much for taking the time to read this. I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface tension. How else could I get a tensionless membrane? As far as I understand, surface tension is only applied when using pcoupl = surface-tension and then ref_p specifies the value of surface tension in bar-nm. Normally, ref_p specifies the reference pressure for an NPT ensemble. As for the generating velocities, I completely forgot that would ruin the equilibrium. Would you recommend saying gen_vel = no or simply raising the gen_temp closer to the required value? If the second how close do you think I should keep it? Sorry for bombarding you guys with so many questions! gen_temp is irrelevant when gen_vel is set to no. Also no one has commented on this so I'm guessing using the structure file from the Berendsen run is an okay way to do what I want? The configuration alone is insufficient. You should preserve the previous ensemble by passing the final .cpt file to grompp -t. -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
[gmx-users] Re: Membrane Equilibration
Is there a reason you would like to keep it at 105K? Just curious which forcefield are you using? Also, for proper surface tension, there is an option called pcoupltype = surface-tension. I think you should check that out. -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038p5009048.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] Re: Membrane Equilibration
Hi, I am using the Martini field for those who wanted to know. My values for the mdp file for ref_p were inspired from this paper as it says pressure was coupled anisotropically to 0 bar in all directions. http://www.sciencedirect.com/science/article/pii/S0005273611002045 I think I will try to set gen_vel = no and see what happens. If it doesn't work I will experiment with altering the ref_p values and surface tension etc. Thank you all for the help! -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038p5009050.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
