hi! Mark warning this.. WARNING 1 [file ../MDP/EM/em_steep_0.mdp]: You are using full electrostatics treatment PME for a system without charges. This costs a lot of performance for just processing zeros, consider using Cut-off instead.
Largest charge group radii for Van der Waals: 0.164, 0.113 nm NOTE 2 [file ../MDP/EM/em_steep_0.mdp]: The sum of the two largest charge group radii (0.276360) is larger than rlist (1.000000) - rvdw (0.900000) ı think no important warning ..isn't it ?.. thanks.......... Date: Mon, 30 Jan 2012 22:25:48 +1100 From: [email protected] To: [email protected] Subject: Re: [gmx-users] simulation killed On 30/01/2012 9:56 PM, murat özçelik wrote: hi! lina my script this.... please tell me where is wrong.......thanks.... Probably your use of -maxwarn is erroneous, unless you can write down why it is valid. Mark #!/bin/bash # Set some environment variables FREE_ENERGY=/home/mkiytak/Free_Energy1 echo "Free energy home directory set to $FREE_ENERGY" MDP=$FREE_ENERGY/MDP echo ".mdp files are stored in $MDP" LAMBDA=0 # A new directory will be created for each value of lambda and # at each step in the workflow for maximum organization. mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA ################################# # ENERGY MINIMIZATION 1: STEEP # ################################# echo "Starting minimization for lambda = $LAMBDA..." mkdir EM_1 cd EM_1 # Iterative calls to grompp and mdrun to run the simulations grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm min$LAMBDA ############################# #### # ENERGY MINIMIZATION 2: L-BFGS # ################################# cd ../ mkdir EM_2 cd EM_2 grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3 # Run L-BFGS in serial (cannot be run in parallel) mdrun -nt 1 -deffnm min$LAMBDA echo "Minimization complete." ##################### # NVT EQUILIBRATION # ##################### echo "Starting constant volume equilibration..." cd ../ mkdir NVT cd NVT grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm nvt$LAMBDA echo "Constant volume equilibration complete." ##################### # NPT EQUILIBRATION # ##################### echo "Starting constant pressure equilibration..." cd ../ mkdir NPT cd NPT grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm npt$LAMBDA echo "Constant pressure equilibration complete." ################# # PRODUCTION MD # ################# echo "Starting production MD simulation..." cd ../ mkdir Production_MD cd Production_MD grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm md$LAMBDA echo "Production MD complete." # End echo "Ending. Job completed for lambda = $LAMBDA" > Date: Mon, 30 Jan 2012 13:54:18 +0800 > Subject: Re: [gmx-users] simulation killed > From: [email protected] > To: [email protected] > > On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900@hotm ail.com> wrote: > > hi again.... capacity of my harddisk 600 GB.... ı try again ..the program > > gave me below message... > > > > Reading file md0.tpr, VERSION 4.5.4 (single precision) > > Starting 8 threads > > > > NOTE: The load imbalance in PME FFT and solve is 1211%. > > For optimal PME load balancing > > PME grid_x (1152) and grid_y (1152) should be divisible by > > #PME_nodes_x (8) > > and PME grid_y (1152) and grid_z (1152) should be divisible by > > #PME_nodes_y (1) > > > > > > Making 1D domain decomposition 8 x 1 x 1 > > starting mdrun 'Protein in water' > > > 2500000 steps, 5000.0 ps. > > ./job_0.sh: line 95: 15777 Killed mdrun -nt 8 -deffnm > > What's inside your job_0.sh? > > something wrong your script. > > > md$LAMBDA > > > > Production MD complete. > > Ending. Job completed for lambda = 0 > > mkiytak@babil:~/JOB1$ > > > > > > How can I solve this problem....thanks for your help..... > > > > > > > > > > > > > > > >> Date: Sun, 29 Jan 2012 10:43:53 -0600 > >> From: [email protected] > >> To: [email protected] > >> Subject: Re: [gmx-users] simulation killed > > > >> > >> something killed your job but it wasn't gromacs. > >> Your system has run time or memory requirements that your job exceeded. > >> > >> On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote: > >> > hi! all > >> > > >> > ı have to a big problem..ı am doing free energy calculation for a ligand > >> > (L > >> > histidine ) when ı perform mdrun .. my simulation stop ... the program > >> > gave > >> > me this message.. > >> > > >> > Reading file md0.tpr, VERSION 4.5.4 (single precision) > >> > Starting 8 threads > >> > Making 1D domain decomposition 8 x 1 x 1 > > & gt; > starting mdrun 'Protein in water' > > > >> > 2500000 steps, 5000.0 ps. > >> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm > >> > md$LAMBDA > >> > Production MD complete. > >> > Ending. Job completed for lambda = 0 > >> > mkiytak@babil:~/JOB1$ > >> > > >> > > >> > my mdp file.. > >> > ; > >> > ; Run control > >> > integrator = sd ; Langevin dynamics > >> > tinit = 0 > >> > dt = 0.002 > >> > nsteps = 2500000 ; 5 ns > >> > nstcomm = 100 > >> > ; Output control > >> > nstxout = 500 > >> > nstvout = 500 > >> > nstfout = 0 > >> > nstlog = 500 > >> > nstenergy = 500 > >> > nstxtcout = 0 > >> > xtc-precision = 1000 > >> > ; Neighborsearching and short-range nonbonded interactions > >> > nstlist = 10 > >> > ns_type = grid > >> > pbc = xyz > >> > rlist = 1.0 > >> > ; Electrostatics > >> > coulombtype = PME > >> > rcoulomb = 1.0 > >> > ; van der Waals > >> > vdw-type = switch > >> > rvdw-switch = 0.8 > >> > rvdw = 0.9 > >> > ; Apply long range dispersion corrections for Energy and Pressure > >> > DispCorr = EnerPres > >> > ; Spacing for the PME/PPPM FFT grid > >> > fourierspacing = 0.12 > >> > ; EWALD/PME/PPPM parameters > >> > pme_order = 6 > >> > ewald_rtol = 1e-06 > >> > epsilon_surface = 0 > >> > optimize_fft = no > >> &g t; ; Temperature coupling > > > >> > ; tcoupl is implicitly handled by the sd integrator > >> > tc_grps = system > >> > tau_t = 1.0 > >> > ref_t = 300 > >> > ; Pressure coupling is on for NPT > >> > Pcoupl = Parrinello-Rahman > >> > tau_p = 0.5 > >> > compressibility = 4.5e-05 > >> > ref_p = 1.0 > >> > ; Free energy control st uff > >> > free_energy = yes > >> > init_lambda = 0.00 > >> > delta_lambda = 0 > >> > foreign_lambda = 0.05 > >> > sc-alpha = 0.5 > >> > sc-power = 1.0 > >> > sc-sigma = 0.3 > >> > couple-moltype = system > >> > couple-lambda0 = vdw ; only van der Waals interactions > >> > couple-lambda1 = non e ; turn off everything, in this case > > > >> > only vdW > >> > couple-intramol = no > >> > nstdhdl = 10 > >> > ; Do not generate velocities > >> > gen_vel = no > >> > ; options for bonds > >> > constraints = h-bonds ; we only have C-H bonds here > >> > ; Type of constraint algorithm > >> > constraint-algorithm = lincs > >> > ; Constrain the starting configuration > >> > ; since we are continuing from NPT > >> > continuation = yes > >> > ; Highest order in the expansion of the constraint coupling matrix > >> > lincs-order = 12 > >> > > >> > PLEASE HELP ME... WHY THE PROGRAM STOP ( KİLLED) SORRY FOR BAD ENGLİSH.. > >> > >> > -- > >> > gmx-users mailing list [email protected] > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to [email protected]. > >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > >> -- > >> =================== =============================================== > >> Peter C. Lai | University of Alabama-Birmingham > >> Programmer/Analyst | KAUL 752A > >> Genetics, Div. of Research | 705 South 20th Street > >> [email protected] | Birmingham AL 35294-4461 > >> (205) 690-0808 | > >> ================================================================== > >> > >> -- > >> gmx-users mailing list [email protected] > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)s ubscribe requests to the list. Use the > >> www interface or send it to [email protected]. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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