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hi again.... capacity of my harddisk 600 GB.... ý try again ..the program gave me below message...<br>Reading file md0.tpr, VERSION 4.5.4 (single precision)<br>Starting 8 threads<br><br>NOTE: The load imbalance in PME FFT and solve is 1211%.<br> For optimal PME load balancing<br> PME grid_x (1152) and grid_y (1152) should be divisible by #PME_nodes_x (8)<br> and PME grid_y (1152) and grid_z (1152) should be divisible by #PME_nodes_y (1)<br><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: 15777 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><span id="result_box" class="short_text" lang="en"><span cla
ss="hps">How can I solve</span> <span class="hps">this</span> <span class="hps">problem....thanks for your help.....</span></span><br><br><br><br><br><br><br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Sun, 29 Jan 2012 10:43:53 -0600<br>> From: pcl@uab.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] simulation killed<br>> <br>> something killed your job but it wasn't gromacs.<br>> Your system has run time or memory requirements that your job exceeded.<br>> <br>> On 2012-01-29 06:40:29PM +0200, mehmet kýytak wrote:<br>> > hi! all<br>> > <br>> > ý have to a big problem..ý am doing free energy calculation for a ligand (L<br>> > histidine ) when ý perform mdrun .. my simulation stop ... the program gave<br>> > 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>&
gt; > starting mdrun 'Protein in water'<br>> > 2500000 steps, 5000.0 ps.<br>> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm<br>> > 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>> &g
t; ; 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 = non
e ; turn off everything, in this case<br>> > 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>> <br>> > -- <br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the
archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> <br>> <br>> -- <br>> ==================================================================<br>> Peter C. Lai | University of Alabama-Birmingham<br>> Programmer/Analyst | KAUL 752A<br>> Genetics, Div. of Research | 705 South 20th Street<br>> pcl@uab.edu | Birmingham AL 35294-4461<br>> (205) 690-0808 |<br>> ==================================================================<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)s
ubscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div> </div></body>
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