Given the unfavorable input, then, it seems odd then that the same .mdp and protein ran consistently on 4.0.7, and I can't seem to find anything in the changelog to indicate a relevant change.
On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 26/01/2012 5:10 PM, Alex Seling wrote: > > Hello, > > After upgrading to gromacs 4.5.5, the old .mdp file that was working is > now giving me errors. > > > Marginally stable numerical integration can work out, or not. Here, you > are using a time step that is not suitable for a simulation lacking bond > constraints. See section 6.5 of manual, for example. If you really want > infinite cut-offs, read 7.3.9. Normal practice to avoid problems is to use > an equilibration regime whose integration scheme is more gentle than your > simulation regime. > > Mark > > > Specifically, I'm getting > "This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size" > for a few interactions, with each of them approaching inf. > > This is with a good starting configuration. Any ideas as to the error? > My .mdp file is below. > > Thanks, > Alex Seling > > > title = lea at 300K > cpp = /lib/cpp -traditional > integrator = md ;sd ;md ;bd > tinit = 0.0 > dt = 0.001 ;time step of 1 fs > nsteps = 238000000 ;1 us @ 1fs > nstxout = 200000 ; frequency to write coordinates to output trajectory > file = 1ns > nstxtcout = 200000 ; frequency to write coordinates to xtc trajectory = 1 > ns > nstvout = 0 > nstfout = 0 > nstlog = 200000 ; frequency to write energies to log file = 1 ns > nstenergy = 200000 ; frequency to write energies to energy file = 1ns > energygrps = system > comm_mode = angular > nstcomm = 40 > nstlist = 100 > nstype = simple > pbc = no > rlist = 100 > rgbradii = 100 > coulombtype = cut-off > epsilon_r = 1 ; double check this is what we want > rcoulomb = 100 > vdwtype = cut-off > rvdw = 100 > tc-grps = system > tau_t = 0.01099 > ref_t = 300 > gen_vel = yes > gen_temp = 273 > constraints = none > implicit_solvent = GBSA > gb_algorithm = OBC > gb_epsilon_solvent = 78 > > > > > > -- > gmx-users mailing list gmx-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 mailing list gmx-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
