zhang wrote: > > Dear all > Thank you for browsing my question.When I run a K ion channel, I added > DOPC bilayer membrane, at the first mdrun, Gromacs program got Range checking > error: > > Explanation: During neighborsearching, we assign each particle to a grid > based on its coordinates. If your system contains collisions or parameter > errors that give particles very high velocities you might end up with some > coordinates being +-Infinity or NaN (not-a-number).
Probably, you have colliging atoms. If two atoms have a distance of less than approx 0.1nm you sometimes run into this error (check with g_mindist). You can also try to switch from steep to cg (or vice versa) as integrator. Jochen > Obviously, we cannot > put these on a grid, so this is usually where we detect those errors. > Make sure your system is properly energy-minimized and that the potential > energy seems reasonable before trying again. > Variable ci has value -2147483648. It should have been within [ 0 .. 24389 ] > Why this error appears? > My em.mdp > > title = comp_dop_water > cpp = /lib/cpp; locationof cpp on SGI > define = -DFLEX_SPC > freezegrps = protein > freezedim = y y y > constraints = none > integrator = steep > dt = 0.002 > nsteps = 3000 > nstlist = 10 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.0 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; > ; energy minimizing stuff > ; > emtol = 1000.0 > emstep = 0.01 > > > Thank you! > > > ? > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
