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On 30/01/2012 9:56 PM, murat özçelik wrote:
<blockquote cite="mid:SNT142-W446B0FE7878501E9150BC9EF8D0@phx.gbl"
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hi! lina my script this.... please tell me where is
wrong.......thanks....<br>
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<br>
Probably your use of -maxwarn is erroneous, unless you can write
down why it is valid.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:SNT142-W446B0FE7878501E9150BC9EF8D0@phx.gbl"
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<br>
#!/bin/bash<br>
<br>
# Set some environment variables <br>
FREE_ENERGY=/home/mkiytak/Free_Energy1<br>
echo "Free energy home directory set to $FREE_ENERGY"<br>
<br>
MDP=$FREE_ENERGY/MDP<br>
echo ".mdp files are stored in $MDP"<br>
<br>
LAMBDA=0<br>
<br>
# A new directory will be created for each value of lambda and<br>
# at each step in the workflow for maximum organization.<br>
<br>
mkdir Lambda_$LAMBDA<br>
cd Lambda_$LAMBDA<br>
<br>
#################################<br>
# ENERGY MINIMIZATION 1: STEEP #<br>
#################################<br>
echo "Starting minimization for lambda = $LAMBDA..." <br>
<br>
mkdir EM_1 <br>
cd EM_1<br>
<br>
# Iterative calls to grompp and mdrun to run the simulations<br>
<br>
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<br>
<br>
mdrun -nt 8 -deffnm min$LAMBDA<br>
<br>
<br>
############################# ####<br>
# ENERGY MINIMIZATION 2: L-BFGS #<br>
#################################<br>
<br>
cd ../<br>
mkdir EM_2<br>
cd EM_2<br>
<br>
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<br>
<br>
# Run L-BFGS in serial (cannot be run in parallel)<br>
<br>
mdrun -nt 1 -deffnm min$LAMBDA<br>
<br>
echo "Minimization complete."<br>
<br>
<br>
<br>
#####################<br>
# NVT EQUILIBRATION #<br>
#####################<br>
echo "Starting constant volume equilibration..."<br>
<br>
cd ../<br>
mkdir NVT<br>
cd NVT<br>
<br>
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<br>
<br>
mdrun -nt 8 -deffnm nvt$LAMBDA<br>
<br>
echo "Constant volume equilibration complete."<br>
<br>
<br>
<br>
#####################<br>
# NPT EQUILIBRATION #<br>
#####################<br>
echo "Starting constant pressure equilibration..."<br>
<br>
cd ../<br>
mkdir NPT<br>
cd NPT<br>
<br>
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$LAMBDA.tpr -maxwarn 3<br>
<br>
mdrun -nt 8 -deffnm npt$LAMBDA<br>
<br>
echo "Constant pressure equilibration complete."<br>
<br>
<br>
#################<br>
# PRODUCTION MD #<br>
#################<br>
echo "Starting production MD simulation..."<br>
<br>
cd ../<br>
mkdir Production_MD<br>
cd Production_MD<br>
<br>
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$LAMBDA.tpr -maxwarn 3<br>
<br>
mdrun -nt 8 -deffnm md$LAMBDA<br>
<br>
echo "Production MD complete."<br>
<br>
# End<br>
echo "Ending. Job completed for lambda = $LAMBDA"<br>
<br>
<div>> Date: Mon, 30 Jan 2012 13:54:18 +0800<br>
> Subject: Re: [gmx-users] simulation killed<br>
> From: <a class="moz-txt-link-abbreviated" href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <br>
> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik
<a class="moz-txt-link-rfc2396E" href="mailto:mehmet63900@hotmail.com"><mehmet63900@hotm ail.com></a> wrote:<br>
> > hi again.... capacity of my harddisk 600 GB.... ı
try again ..the program<br>
> > gave me below message...<br>
> ><br>
> > Reading file md0.tpr, VERSION 4.5.4 (single
precision)<br>
> > Starting 8 threads<br>
> ><br>
> > NOTE: The load imbalance in PME FFT and solve is
1211%.<br>
> > For optimal PME load balancing<br>
> > PME grid_x (1152) and grid_y (1152) should be
divisible by<br>
> > #PME_nodes_x (8)<br>
> > and PME grid_y (1152) and grid_z (1152) should
be divisible by<br>
> > #PME_nodes_y (1)<br>
> ><br>
> ><br>
> > Making 1D domain decomposition 8 x 1 x 1<br>
> > starting mdrun 'Protein in water'<br>
> <br>
> > 2500000 steps, 5000.0 ps.<br>
> > ./job_0.sh: line 95: 15777 Killed
mdrun -nt 8 -deffnm<br>
> <br>
> What's inside your job_0.sh?<br>
> <br>
> something wrong your script.<br>
> <br>
> > md$LAMBDA<br>
> ><br>
> > Production MD complete.<br>
> > Ending. Job completed for lambda = 0<br>
> > mkiytak@babil:~/JOB1$<br>
> ><br>
> ><br>
> > How can I solve this problem....thanks for your
help.....<br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> >> Date: Sun, 29 Jan 2012 10:43:53 -0600<br>
> >> From: <a class="moz-txt-link-abbreviated" href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>
> >> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> Subject: Re: [gmx-users] simulation killed<br>
> ><br>
> >><br>
> >> something killed your job but it wasn't gromacs.<br>
> >> Your system has run time or memory requirements
that your job exceeded.<br>
> >><br>
> >> On 2012-01-29 06:40:29PM +0200, mehmet kıytak
wrote:<br>
> >> > hi! all<br>
> >> ><br>
> >> > ı have to a big problem..ı am doing free
energy calculation for a ligand<br>
> >> > (L<br>
> >> > histidine ) when ı perform mdrun .. my
simulation stop ... the program<br>
> >> > gave<br>
> >> > me this message..<br>
> >> ><br>
> >> > Reading file md0.tpr, VERSION 4.5.4 (single
precision)<br>
> >> > Starting 8 threads<br>
> >> > Making 1D domain decomposition 8 x 1 x 1<br>
> > & gt; > starting mdrun 'Protein in water'<br>
> ><br>
> >> > 2500000 steps, 5000.0 ps.<br>
> >> > ./job_0.sh: line 95: 15457 Killed mdrun -nt
8 -deffnm<br>
> >> > md$LAMBDA<br>
> >> > Production MD complete.<br>
> >> > Ending. Job completed for lambda = 0<br>
> >> > mkiytak@babil:~/JOB1$<br>
> >> ><br>
> >> ><br>
> >> > my mdp file..<br>
> >> > ;<br>
> >> > ; Run control<br>
> >> > integrator = sd ; Langevin dynamics<br>
> >> > tinit = 0<br>
> >> > dt = 0.002<br>
> >> > nsteps = 2500000 ; 5 ns<br>
> >> > nstcomm = 100<br>
> >> > ; Output control<br>
> >> > nstxout = 500<br>
> >> > nstvout = 500<br>
> >> > nstfout = 0<br>
> >> > nstlog = 500<br>
> >> > nstenergy = 500<br>
> >> > nstxtcout = 0<br>
> >> > xtc-precision = 1000<br>
> >> > ; Neighborsearching and short-range
nonbonded interactions<br>
> >> > nstlist = 10<br>
> >> > ns_type = grid<br>
> >> > pbc = xyz<br>
> >> > rlist = 1.0<br>
> >> > ; Electrostatics<br>
> >> > coulombtype = PME<br>
> >> > rcoulomb = 1.0<br>
> >> > ; van der Waals<br>
> >> > vdw-type = switch<br>
> >> > rvdw-switch = 0.8<br>
> >> > rvdw = 0.9<br>
> >> > ; Apply long range dispersion corrections
for Energy and Pressure<br>
> >> > DispCorr = EnerPres<br>
> >> > ; Spacing for the PME/PPPM FFT grid<br>
> >> > fourierspacing = 0.12<br>
> >> > ; EWALD/PME/PPPM parameters<br>
> >> > pme_order = 6<br>
> >> > ewald_rtol = 1e-06<br>
> >> > epsilon_surface = 0<br>
> >> > optimize_fft = no<br>
> >> &g t; ; Temperature coupling<br>
> ><br>
> >> > ; tcoupl is implicitly handled by the sd
integrator<br>
> >> > tc_grps = system<br>
> >> > tau_t = 1.0<br>
> >> > ref_t = 300<br>
> >> > ; Pressure coupling is on for NPT<br>
> >> > Pcoupl = Parrinello-Rahman<br>
> >> > tau_p = 0.5<br>
> >> > compressibility = 4.5e-05<br>
> >> > ref_p = 1.0<br>
> >> > ; Free energy control st uff<br>
> >> > free_energy = yes<br>
> >> > init_lambda = 0.00<br>
> >> > delta_lambda = 0<br>
> >> > foreign_lambda = 0.05<br>
> >> > sc-alpha = 0.5<br>
> >> > sc-power = 1.0<br>
> >> > sc-sigma = 0.3<br>
> >> > couple-moltype = system<br>
> >> > couple-lambda0 = vdw ; only van der Waals
interactions<br>
> >> > couple-lambda1 = non e ; turn off
everything, in this case<br>
> ><br>
> >> > only vdW<br>
> >> > couple-intramol = no<br>
> >> > nstdhdl = 10<br>
> >> > ; Do not generate velocities<br>
> >> > gen_vel = no<br>
> >> > ; options for bonds<br>
> >> > constraints = h-bonds ; we only have C-H
bonds here<br>
> >> > ; Type of constraint algorithm<br>
> >> > constraint-algorithm = lincs<br>
> >> > ; Constrain the starting configuration<br>
> >> > ; since we are continuing from NPT<br>
> >> > continuation = yes<br>
> >> > ; Highest order in the expansion of the
constraint coupling matrix<br>
> >> > lincs-order = 12<br>
> >> ><br>
> >> > PLEASE HELP ME... WHY THE PROGRAM STOP (
KİLLED) SORRY FOR BAD ENGLİSH..<br>
> >><br>
> >> > --<br>
> >> > gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> >
<a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> >> > Please search the archive at<br>
> >> >
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before
posting!<br>
> >> > Please don't post (un)subscribe requests to
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> >> > www interface or send it to
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> >> > Can't post? Read
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> >><br>
> >><br>
> >> --<br>
> >> ===================
===============================================<br>
> >> Peter C. Lai | University of Alabama-Birmingham<br>
> >> Programmer/Analyst | KAUL 752A<br>
> >> Genetics, Div. of Research | 705 South 20th
Street<br>
> >> <a class="moz-txt-link-abbreviated" href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
> >> (205) 690-0808 |<br>
> >>
==================================================================<br>
> >><br>
> >> --<br>
> >> gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >>
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> >> Please search the archive at<br>
> >>
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posting!<br>
> >> Please don't post (un)s ubscribe requests to the
list. Use the<br>
> >> www interface or send it to
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> >> Can't post? Read
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
> ><br>
> > --<br>
> > gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> > <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at<br>
> > <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
> > Please don't post (un)subscribe requests to the
list. Use the<br>
> > www interface or send it to
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
> -- <br>
> gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before
posting!<br>
> Please don't post (un)subscribe requests to the list. Use
the <br>
> www interface or send it to
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
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