[gmx-users] simulation killed
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Jan 30 21:06:30 CET 2012
On 31/01/2012 12:15 AM, mehmet k?ytak wrote:
>
> 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.
So for a quick EM, you don't care about performance, so using PME with
no charges can be acceptable. However, changing your EM .mdp to cut-off
avoids the warning entirely, and there is no change in the result of the
computation.
>
>
> 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)
>
> ? think no important warning ..isn't it ?..
> thanks..........
Having two or more large charge groups can mean your model of VDW
interactions is inaccurate, because you can be failing to compute
interactions that are closer than rvdw. You should use smaller charge
groups (which is probably the right approach for your force field once
you are no longer doing EM and/or are using charges).
If there's no third warning, then you should definitely not use -maxwarn
3, because sometime later when you adapt this script inappropriately and
create a new warning while perhaps removing an existing one, then you
are silently avoiding making a decision about whether the new warning
matters. This is why fixing the cause of warnings and not the symptoms
is wise.
Mark
>
>
> ------------------------------------------------------------------------
>
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>
> Date: Mon, 30 Jan 2012 22:25:48 +1100
>
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> 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 = $LAMBDA"
>
> > Date: Mon, 30 Jan 2012 13:54:18 +0800
> > Subject: Re: [gmx-users] simulation killed
> > From: lina.lastname at gmail.com <mailto:lina.lastname at gmail.com>
> > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> >
> > On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900 at hotm
> ail.com> <mailto:mehmet63900 at hotmail.com> wrote:
> > > hi again.... capacity of my harddisk 600 GB.... ? try again
> ..the program
> > > gave me below message...
> > >
> > > Reading file md0.tpr, VERSION 4.5.4 (single precision)
> > > Starting 8 threads
> > >
> > > NOTE: The load imbalance in PME FFT and solve is 1211%.
> > > For optimal PME load balancing
> > > PME grid_x (1152) and grid_y (1152) should be divisible by
> > > #PME_nodes_x (8)
> > > and PME grid_y (1152) and grid_z (1152) should be
> divisible by
> > > #PME_nodes_y (1)
> > >
> > >
> > > Making 1D domain decomposition 8 x 1 x 1
> > > starting mdrun 'Protein in water'
> >
> > > 2500000 steps, 5000.0 ps.
> > > ./job_0.sh: line 95: 15777 Killed mdrun -nt
> 8 -deffnm
> >
> > What's inside your job_0.sh?
> >
> > something wrong your script.
> >
> > > md$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 <mailto:pcl at uab.edu>
> > >> To: gmx-users at gromacs.org <mailto: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 k?ytak wrote:
> > >> > hi! all
> > >> >
> > >> > ? have to a big problem..? am doing free energy calculation
> for a ligand
> > >> > (L
> > >> > histidine ) when ? 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 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 ( KI.LLED) SORRY FOR
> BAD ENGLI.SH..
> > >>
> > >> > --
> > >> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > >> > Please search the archive at
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> > >>
> > >>
> > >> --
> > >> ===================
> ===============================================
> > >> Peter C. Lai | University of Alabama-Birmingham
> > >> Programmer/Analyst | KAUL 752A
> > >> Genetics, Div. of Research | 705 South 20th Street
> > >> pcl at uab.edu <mailto:pcl at uab.edu> | Birmingham AL 35294-4461
> > >> (205) 690-0808 |
> > >>
> ==================================================================
> > >>
> > >> --
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> > >
> > > --
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