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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