[gmx-users] Fw: mdrun failure

fatemeh ramezani fr_750 at yahoo.com
Tue May 23 10:34:48 CEST 2017

 Hi dear gmx-usersIwant to simulate gold surface - protein interaction by GOLP-CHARMM forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp contains: title                   = goldcpp                     =cppinclude                 =  ;RUN CONTROL PARAMETERSintegrator              = md  ;ENERGY MINIMIZATION OPTIONSemtol                   = 500.0emstep                  = 0.001tinit                   = 0.000dt                      =0.001nsteps = 100000 ;OUTPUT CONTROL OPTIONSnstxout                 = 3000nstvout                 = 3000nstfout                 = 0nstlog                  = 1nstenergy               = 3000 ;Output frequency and precision for xtc filenstxtcout               = 3000xtc-precision           = 3000 ;NEIGHBORSEARCHING PARAMETERS;Periodic boundary conditions: xyz (default), no (vacuum)pbc                     =xyzperiodic_molecules      = yesrlist                   = 1.10 ;OPTIONS FOR ELECTROSTATICS AND VDW;Method for doing electrostaticscoulombtype             = PMEr_coulomb                = 1.1ewald_rtol              = 1e-06ewald_geometry          = 3d ;Method for doing Van der Waalsvdw-type                = switchrvdw-switch             = 0.90rvdw                    = 1.10 ;OPTIONS FOR BONDS    constraints             = h-bondsconstraint-algorithm    = Lincslincs-order             = 8lincs-iter              = 12;Lincs will write a warning to the stderr if in one step a bond;rotates over more degrees thanlincs-warnangle         = 90 ;OPTIONS FOR WEAK COUPLING ALGORITHMS;Temperature coupling  Tcoupl                  = Nose-Hoovernhchainlength = 1;Groups to couple separatelytc-grps                 = Protein  Non-Protein;Time constant (ps) and reference temperature (K)tau-t                   = 0.2 0.2ref-t                   = 310 310 ;Non-equilibrium MD stufffreezegrps              = slabfreezedim               = Y Y Y mdrun command is: nohup mdrun -smd.tpr -o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin on -pinoffset 1 & the last line of md.logis: Step          Time         Lambda          7460        7.46000       0.00000    Energies(kJ/mol)           U-B    Proper Dih.  Improper Dih.     CMAP Dih.          LJ-14   5.39081e+04    1.47221e+04    3.15826e+03  -1.85050e+03    1.80904e+04    Coulomb-14        LJ (SR)   Coulomb (SR)  Coul. recip.      Potential   2.97824e+05    2.17254e+12   -6.91585e+06   3.01612e+04    2.17254e+12    KineticEn.   Total Energy  Conserved En.    Temperature Pressure(bar)   7.71065e+14    7.73237e+14    9.41950e+16   2.61554e+11    2.41578e+12   Constr.rmsd   1.15453e-01 The last line ofnohup.out is:  Changing nstlist from 10to 40, rlist from 1.1 to 1.1 Using 1 MPI threadUsing 3 OpenMP threadsApplying core pinningoffset 1Setting the maximumnumber of constraint warnings to -1 Back Off! I just backedup fws_md3.trr to ./#fws_md3.trr.20# Back Off! I just backedup traj_comp.xtc to ./#traj_comp.xtc.22# Back Off! I just backedup md3.edr to ./#md3.edr.20#starting mdrun 'Proteinin water'100000 steps,   100.0 ps. Can you help me toprevent from mdrun failing?Thank you very much 
 Fatemeh Ramezani


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