Re: [gmx-users] simulation killed

Justin A. Lemkul Mon, 30 Jan 2012 05:24:14 -0800


lina wrote:

did you write this script yourself?

This script appears to be based on one that I provided in the free energytutorial, but there are some differences (including one of the mistakes you notebelow). It would be helpful if the OP explained what these simulations weredoing, as well as if they are attempting the tutorial or some other differentsystem.


-Justin

On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik <[email protected]> wrote:

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.

Here add:

if [ -d "Lambda_$LAMBDA" ]; then
        rm -r Lambda_$LAMBDA
fi

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


One thing, do you use  define         = -DPOSRES in your nvt_0.mdp, if
yes, you need take care where your posre.itp file stored.

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


Here "$ LAMBDA" --> "$LAMBDA", no space.

$FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$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..

&gt ;

; 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..
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--
=================== ===============================================
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 |
==================================================================

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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