Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a segmentation fault. GROMACS doesn't waste its time checking for this, since that would hurt everyone's performance and gain only a descriptive error that something is horribly broken!
Mark On Nov 28, 2013 1:36 AM, "Valentina" <valentina.erast...@durham.ac.uk> wrote: > I still cannot resolve this problem. Is there any way to find out what is > causing Segmentation Fault? Normally Gromacs provides quite comprehendible > errors, but this one. > > I have checked the charges against DFT. > > I also have the output of the system simulated with Discover. I am using > that force field (obviously tabulated) and charges used there. > > The initial model is taken from Xray and optimised with DFT. > > Still md.log terminates with unrealistic T & P on 0th step: > > / Step Time Lambda > 0 0.00000 0.00000 > > > Grid: 4 x 3 x 3 cells > Energies (kJ/mol) > Tab. Bonds Tab. Angles LJ (SR) Coulomb (SR) Potential > 5.44943e+06 4.41001e+11 9.86202e+02 -2.42548e+05 4.41006e+11 > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar) > 1.97584e+16 1.97588e+16 1.97588e+16 2.24716e+15 1.99874e+16 > / > > > BTW - I noticed that I get continuously get a 0 dimension in z direction if > I do energy minimisation with plc = xy - is that right? > > My equil.mdp is following - may be some problem there? > I do energy minimisation before equilibration. > > /integrator = md > nsteps = 100 > dt = 0.001 > ;comm_mode = ANGULAR > nstenergy = 1 > nstxout = 1 > nstvout = 1 > energygrps = System > ; cut-offs at 1nm > rlist = 0.8 > nstlist = 10 > coulombtype = user > rcoulomb = 0.8 > vdw-type = user > rvdw = 0.8 > pbc = xyz > periodic_molecules = yes > ; set temperature to 300K > tcoupl = V-rescale > tc-grps = System > tau-t = 1.0 > ref-t = 500 > ; and pressure to 1 bar > pcoupl = no > compressibility = 4.5e-5 > ; generate initial velocities > gen-vel = no/ > > I am running with 6-9 LJ, that I provide input to mdrun > > > > > I do energy minimisation before equilibration. > em.mdp is > /integrator = steep > nsteps = 500000 > emtol = 1 > emstep = 0.001 > nstxout = 1 > nstenergy = 1 > rlist = 0.8 > pbc = xyz > periodic_molecules = yes > coulombtype = user > rcoulomb = 0.8 > vdw-type = user > rvdw = 0.8 > constraints = none/ > > > I get following output: > > /Steepest Descents: > Tolerance (Fmax) = 1.00000e+00 > Number of steps = 500000 > Step= 2, Dmax= 5.0e-04 nm, Epot= 4.40635e+11 Fmax= 8.77355e+10, atom= > 223 > Step= 4, Dmax= 3.0e-04 nm, Epot= 4.40403e+11 Fmax= 9.61163e+10, atom= > 263 > Step= 6, Dmax= 1.8e-04 nm, Epot= 4.40248e+11 Fmax= 1.01812e+11, atom= > 833 > Step= 8, Dmax= 1.1e-04 nm, Epot= 4.40181e+11 Fmax= 9.36260e+10, atom= > 83 > Step= 10, Dmax= 6.5e-05 nm, Epot= 4.40142e+11 Fmax= 9.89456e+10, atom= > 833 > Step= 12, Dmax= 3.9e-05 nm, Epot= 4.40115e+11 Fmax= 8.24990e+10, atom= > 105 > Step= 14, Dmax= 2.3e-05 nm, Epot= 4.40094e+11 Fmax= 4.88140e+10, atom= > 105 > Step= 19, Dmax= 1.7e-06 nm, Epot= 4.40098e+11 Fmax= 4.47573e+10, atom= > 223 > Energy minimization has stopped, but the forces havenot converged to the > requested precision Fmax < 1 (whichmay not be possible for your system). It > stoppedbecause the algorithm tried to make a new step whose sizewas too > small, or there was no change in the energy sincelast step. Either way, we > regard the minimization asconverged to within the available machine > precision,given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, butthis is often not > needed for preparing to run moleculardynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Back Off! I just backed up confout.gro to ./#confout.gro.4# > > Steepest Descents converged to machine precision in 20 steps, > but did not reach the requested Fmax < 1. > Potential Energy = 4.4009390e+11 > Maximum force = 4.8813974e+10 on atom 105 > Norm of force = 5.4008571e+09 > / > > I cannot recollect how energy minimisation output should look like - is > this > right? > > > It would be great to hear some suggestions how to pin-point the problem. > > Thank you for your help > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/step-0Segmentation-fault-11-tp5012832p5012866.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.