[gmx-users] simulation killed

Mon Jan 30 11:56:04 CET 2012

hi! lina my script this.... please tell me where is wrong.......thanks....

#!/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: lina.lastname at gmail.com
> To: gmx-users at gromacs.org
> 
> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900 at hotmail.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$LAMBDA
> >
> > Production MD complete.
> > Ending. Job completed for lambda = 0
> > mkiytak at babil:~/JOB1$
> >
> >
> > How can I solve this problem....thanks for your help.....
> >
> >
> >
> >
> >
> >
> >
> >> Date: Sun, 29 Jan 2012 10:43:53 -0600
> >> From: pcl at uab.edu
> >> To: gmx-users at gromacs.org
> >> 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$LAMBDA
> >> > Production MD complete.
> >> > Ending. Job completed for lambda = 0
> >> > mkiytak at babil:~/JOB1$
> >> >
> >> >
> >> > 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 stuff
> >> > 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 gmx-users at gromacs.org
> >> > 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 gmx-users-request at gromacs.org.
> >> > 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
> >> pcl at uab.edu | Birmingham AL 35294-4461
> >> (205) 690-0808 |
> >> ==================================================================
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
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> >
> > --
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