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
------------------------------------------------------------------------
Date: Mon, 30 Jan 2012 22:25:48 +1100
From: mark.abra...@anu.edu.au
To: gmx-users@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 = $LAMBDA"
> Date: Mon, 30 Jan 2012 13:54:18 +0800
> Subject: Re: [gmx-users] simulation killed
> From: lina.lastn...@gmail.com <mailto:lina.lastn...@gmail.com>
> To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
>
> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900@hotm
ail.com> <mailto:mehmet63...@hotmail.com> wrote:
> > hi again.... capacity of my harddisk 600 GB.... ? try again
..the program
> > gave me below message...
> >
> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
> > Starting 8 threads
> >
> > NOTE: The load imbalance in PME FFT and solve is 1211%.
> > For optimal PME load balancing
> > PME grid_x (1152) and grid_y (1152) should be divisible by
> > #PME_nodes_x (8)
> > and PME grid_y (1152) and grid_z (1152) should be
divisible by
> > #PME_nodes_y (1)
> >
> >
> > Making 1D domain decomposition 8 x 1 x 1
> > starting mdrun 'Protein in water'
>
> > 2500000 steps, 5000.0 ps.
> > ./job_0.sh: line 95: 15777 Killed mdrun -nt
8 -deffnm
>
> What's inside your job_0.sh?
>
> something wrong your script.
>
> > md$LAMBDA
> >
> > Production MD complete.
> > Ending. Job completed for lambda = 0
> > mkiytak@babil:~/JOB1$
> >
> >
> > How can I solve this problem....thanks for your help.....
> >
> >
> >
> >
> >
> >
> >
> >> Date: Sun, 29 Jan 2012 10:43:53 -0600
> >> From: p...@uab.edu <mailto:p...@uab.edu>
> >> To: gmx-users@gromacs.org <mailto:gmx-users@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$LAMBDA
> >> > Production MD complete.
> >> > Ending. Job completed for lambda = 0
> >> > mkiytak@babil:~/JOB1$
> >> >
> >> >
> >> > 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@gromacs.org
<mailto:gmx-users@gromacs.org>
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >> > www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@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
> >> p...@uab.edu <mailto:p...@uab.edu> | Birmingham AL 35294-4461
> >> (205) 690-0808 |
> >>
==================================================================
> >>
> >> --
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