hi! all<br><br>ý have to a big problem..ý am doing free energy calculation for a ligand (L histidine ) when ý perform mdrun .. my simulation stop ... the program gave me this message..<br><br>Reading file md0.tpr, VERSION 4.5.4 (single precision)<br>
Starting 8 threads<br>Making 1D domain decomposition 8 x 1 x 1<br>starting mdrun 'Protein in water'<br>2500000 steps, 5000.0 ps.<br>./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm md$LAMBDA<br>
Production MD complete.<br>Ending. Job completed for lambda = 0<br>mkiytak@babil:~/JOB1$ <br> <br><br>my mdp file..<br><br>; Run control<br>integrator = sd ; Langevin dynamics<br>tinit = 0<br>
dt = 0.002<br>nsteps = 2500000 ; 5 ns<br>nstcomm = 100<br>; Output control<br>nstxout = 500<br>nstvout = 500<br>nstfout = 0<br>
nstlog = 500<br>nstenergy = 500<br>nstxtcout = 0<br>xtc-precision = 1000<br>; Neighborsearching and short-range nonbonded interactions<br>nstlist = 10<br>
ns_type = grid<br>pbc = xyz<br>rlist = 1.0<br>; Electrostatics<br>coulombtype = PME<br>rcoulomb = 1.0<br>; van der Waals<br>vdw-type = switch<br>
rvdw-switch = 0.8<br>rvdw = 0.9<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>
; EWALD/PME/PPPM parameters<br>pme_order = 6<br>ewald_rtol = 1e-06<br>epsilon_surface = 0<br>optimize_fft = no<br>; Temperature coupling<br>; tcoupl is implicitly handled by the sd integrator<br>
tc_grps = system<br>tau_t = 1.0<br>ref_t = 300<br>; Pressure coupling is on for NPT<br>Pcoupl = Parrinello-Rahman<br>tau_p = 0.5<br>
compressibility = 4.5e-05<br>ref_p = 1.0<br>; Free energy control stuff<br>free_energy = yes<br>init_lambda = 0.00<br>delta_lambda = 0<br>foreign_lambda = 0.05<br>
sc-alpha = 0.5<br>sc-power = 1.0<br>sc-sigma = 0.3<br>couple-moltype = system<br>couple-lambda0 = vdw ; only van der Waals interactions<br>couple-lambda1 = none ; turn off everything, in this case only vdW<br>
couple-intramol = no<br>nstdhdl = 10<br>; Do not generate velocities<br>gen_vel = no<br>; options for bonds<br>constraints = h-bonds ; we only have C-H bonds here<br>
; Type of constraint algorithm<br>constraint-algorithm = lincs<br>; Constrain the starting configuration<br>; since we are continuing from NPT<br>continuation = yes<br>; Highest order in the expansion of the constraint coupling matrix<br>
lincs-order = 12<br><br>PLEASE HELP ME... WHY THE PROGRAM STOP ( KÝLLED) SORRY FOR BAD ENGLÝSH..<br>