Hey Vivek,
Thanks for the suggestion. I tried this, but I still get the same problem. Cheers, Alex 2014-07-17 17:58 GMT+02:00 vivek sinha <viveksinha20...@gmail.com>: > Hey Alex, > I was also having the same error from two days although my topology files > and mdp files were (I think) correct. Just two hours ago I corrected the > problem. I just changed the timestep from 0.002 to 0.0002 and it worked. > You can also try this. > > Regards, > Vivek Sinha > > > On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo <barrozo...@gmail.com> > wrote: > > > Hi everybody, > > > > > > I am trying to make a simulation of an enzyme containing a metal ion > using > > a dummy model for it. I have inserted all the parameters, generated the > > topology, solvated the system, without any problem. > > > > When I try to run a first equilibration, I get the following warning: > > > > > > > > WARNING: Listed nonbonded interaction between particles 127 and 134* > > at distance 3f which is larger than the table limit 3f nm. > > > > This is likely either a 1,4 interaction, or a listed interaction inside > > a smaller molecule you are decoupling during a free energy calculation. > > Since interactions at distances beyond the table cannot be computed, > > they are skipped until they are inside the table limit again. You will > > only see this message once, even if it occurs for several interactions. > > > > *These particles are close to the dummy model for the metal. I believe > the > > problem might be related to that, but I had no problem in generating > > topologies, or anything like that. > > > > > > After that warning, I have a Segmentation fault. > > > > > > Here is my mdp file for the test equilibration that I was trying: > > > > define = -DPOSRES -DPOSRES_WATER ; position > restrain > > the protein > > ; Run parameters > > integrator = md ; leap-frog > > integrator > > nsteps = 50000 ; 2 * 50000 = 100 > > ps > > dt = 0.001 ; 1 fs > > ; Output control > > nstxout = 500 ; save > coordinates > > every 1.0 ps > > nstvout = 500 ; save velocities > > every 1.0 ps > > nstenergy = 500 ; save energies > > every 1.0 ps > > nstlog = 500 ; update log file > > every 1.0 ps > > ; Bond parameters > > continuation = no ; first dynamics > > run > > ; constraint_algorithm = lincs ; holonomic > > constraints > > constraints = none ; all bonds (even > > heavy atom-H bonds) constrained > > ; Neighborsearching > > cutoff-scheme = Verlet > > ns_type = grid ; search > > neighboring grid cells > > nstlist = 30 ; 20 fs, largely > > irrelevant with Verlet > > rcoulomb = 1.0 ; short-range > > electrostatic cutoff (in nm) > > rvdw = 1.0 ; short-range van > > der Waals cutoff (in nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh > > Ewald for long-range electrostatics > > pme_order = 4 ; cubic > > interpolation > > fourierspacing = 0.16 ; grid spacing > for > > FFT > > ; Temperature coupling is on > > tcoupl = V-rescale ; modified > > Berendsen thermostat > > tc-grps = Protein Non-Protein ; two coupling > > groups - more accurate > > tau_t = 0.1 0.1 ; time constant, > in > > ps > > ref_t = 1 1 ; reference > > temperature, one for each group, in K > > ; Pressure coupling is off > > pcoupl = no ; no pressure > > coupling in NVT > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > ; Dispersion correction > > DispCorr = EnerPres ; account for > > cut-off vdW scheme > > ; Velocity generation > > gen_vel = yes ; assign > velocities > > from Maxwell distribution > > gen_temp = 1 ; temperature for > > Maxwell distribution > > gen_seed = -1 ; generate a > random > > seed > > > > > > > > Any clue about what is going on? > > > > > > Cheers, > > > > Alex > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.