Hi, Well, I tried running a simulation at ref_p to 1.0 and got the same error as earlier, so it doesn't seem to be that. That was the only thing I changed in the mdp file, so I am still not sure as to where the problem is.
Justin Lemkul wrote > On 6/18/13 3:13 PM, Neha wrote: >> 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! >> > > What happens if you set ref_p to 1.0? I don't understand the use of zero > pressure; your system is expanding out into a vacuum and that's likely why > the > z-dimension is expanding uncontrollably. Water diffuses faster than the > lipids, > so the z-dimension expands faster than x-y does. > > -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-Runs-Crashing-tp5009264p5009271.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
