[gmx-users] crash nsgrid.c

[Berk Hess]

Hi,There can be many reasons for such problems.I assume you use solvent.One option is that you could have made your whole proteina single charge group. grompp in Gromacs 3.3.3 checks for this,but older versions do not.Berk.> From: affinito at gmail.com> To: gmx-users at gromacs.org> Date: Thu, 8 May 2008 14:54:27 +0200> Subject: [gmx-users] crash nsgrid.c> > > Dear all,> During my simulations of a GFP protein (force field made with amber,  > then converted to gromacs), I usually get this error:> > Fatal error: ci = 8108 should be in 0 .. 7937 [FILE nsgrid.c, LINE 218]> > What this that means?> > If I restart the simulation from the frame just before the crash, the  > run is ok for a (random) time and then it crashes again.> I checked this on different kind of machines and I get always the same  > behavior.> > To make things clearier, I include the input.mdp file:> > title                    => cpp                      = /lib/cpp> include                  => define                   => integrator               = md> dt                       = 0.002> nsteps                   = 500000> nstxout                  = 10000> nstvout                  = 0> nstlog                   = 500> nstenergy                = 500> nstxtcout                = 500> energygrps               = System> pbc                      = xyz> nstlist                  = 15> epsilon_r                = 1.> ns_type                  = grid> coulombtype              = pme> vdwtype                  = Cut-off> rlist                    = 0.8> rcoulomb                 = 0.8> rvdw                     = 0.8> tcoupl                   = Nose-Hoover> tc-grps                  = System> tau_t                    = 2.0> ref_t                    = 300.00> pcoupl                   = Parrinello-Rahman> pcoupltype               = isotropic> tau_p                    = 4.0> compressibility          = 4.5e-5> ref_p                    = 1.0> gen_vel                  = no> gen_seed                 = 173529> constraints              = All-bonds> constraint_algorithm     = lincs> shake_tol                = 0.0001> > Any suggestion is welcome.> > Thanks> > F.A.> _______________________________________________> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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