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 list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
