Hi everybody! I am trying to simulate a lipid membrane at zero pressure and at a range of temperatures. I am using a bilayer from the Martini website. I was having a problem with the Parinello-Rahman barostat so I switched to Berendsen and am also keeping the height of the box constant otherwise it grows uncontrollably. However my runs keep crashing, giving the error of atoms having moved too far beyond the cut-off distance. I have attached part of my mdp file, and would love any suggestions as to how to alter it to get more fruitful runs. I am still really new to Gromacs and want to make sure I am not doing something completely wrong.
; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = DPPC W ; Time constant (ps) and reference temperature (K) = tau_t = 1.0 1.0 ref_t = 325 325 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 1.0 1.0 compressibility = 5e-6 0.0 ref_p = 0.0 0.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 325 gen_seed = 473529 Please let me know! -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Runs-Crashing-tp5009264.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
