On 11/27/13 7:30 PM, Valentina 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?
No, this outcome is terrible. Energy should (almost) always be negative and the maximum force should be less than the target Fmax. You have massive forces (10^10 - yikes!) on atom 105, indicating either severe problems with the configuration (which should be obvious upon visual inspection) or, again, your tabulated potential is wrong.
Mark's suggestion before is a good one - simplify the system into its most basic units, down to the level of two atoms and build up to verify your input. From the output shown, the only logical explanations are (1) bad tables or (2) bad configuration.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.