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On 31/01/2012 12:15 AM, mehmet kıytak wrote:
<blockquote cite="mid:SNT142-W256677423CC999DF3A43E5EF8D0@phx.gbl"
type="cite">
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<br>
hi! Mark<br>
warning this..<br>
WARNING 1 [file ../MDP/EM/em_steep_0.mdp]:<br>
You are using full electrostatics treatment PME for a system
without<br>
charges.<br>
This costs a lot of performance for just processing zeros,
consider using<br>
Cut-off instead.<br>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote cite="mid:SNT142-W256677423CC999DF3A43E5EF8D0@phx.gbl"
type="cite">
<div dir="ltr"><br>
<br>
Largest charge group radii for Van der Waals: 0.164, 0.113 nm<br>
<br>
NOTE 2 [file ../MDP/EM/em_steep_0.mdp]:<br>
The sum of the two largest charge group radii (0.276360) is
larger than<br>
rlist (1.000000) - rvdw (0.900000)<br>
<br>
ı think no important warning ..isn't it ?.. <br>
thanks..........<br>
</div>
</blockquote>
<br>
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).<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:SNT142-W256677423CC999DF3A43E5EF8D0@phx.gbl"
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Date: Mon, 30 Jan 2012 22:25:48 +1100<br>
<br>
From: <a class="moz-txt-link-abbreviated" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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>
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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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<div dir="ltr"> hi! lina my script this.... please tell me
where is wrong.......thanks....<br>
</div>
</blockquote>
<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">
<div dir="ltr"><br>
<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 = $LAMBDA"<br>
<br>
<div>> Date: Mon, 30 Jan 2012 13:54:18 +0800<br>
> Subject: Re: [gmx-users] simulation killed<br>
> From: <a moz-do-not-send="true"
class="ecxmoz-txt-link-abbreviated"
href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a><br>
> To: <a moz-do-not-send="true"
class="ecxmoz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <br>
> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <a
moz-do-not-send="true"
class="ecxmoz-txt-link-rfc2396E"
href="mailto:mehmet63900@hotmail.com"><mehmet63900@hotm
ail.com></a> wrote:<br>
> > hi again.... capacity of my harddisk 600
GB.... ı try again ..the program<br>
> > gave me below message...<br>
> ><br>
> > Reading file md0.tpr, VERSION 4.5.4 (single
precision)<br>
> > Starting 8 threads<br>
> ><br>
> > NOTE: The load imbalance in PME FFT and solve
is 1211%.<br>
> > For optimal PME load balancing<br>
> > PME grid_x (1152) and grid_y (1152)
should be divisible by<br>
> > #PME_nodes_x (8)<br>
> > and PME grid_y (1152) and grid_z (1152)
should be divisible by<br>
> > #PME_nodes_y (1)<br>
> ><br>
> ><br>
> > Making 1D domain decomposition 8 x 1 x 1<br>
> > starting mdrun 'Protein in water'<br>
> <br>
> > 2500000 steps, 5000.0 ps.<br>
> > ./job_0.sh: line 95: 15777 Killed
mdrun -nt 8 -deffnm<br>
> <br>
> What's inside your job_0.sh?<br>
> <br>
> something wrong your script.<br>
> <br>
> > md$LAMBDA<br>
> ><br>
> > Production MD complete.<br>
> > Ending. Job completed for lambda = 0<br>
> > mkiytak@babil:~/JOB1$<br>
> ><br>
> ><br>
> > How can I solve this problem....thanks for
your help.....<br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> >> Date: Sun, 29 Jan 2012 10:43:53 -0600<br>
> >> From: <a moz-do-not-send="true"
class="ecxmoz-txt-link-abbreviated"
href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>
> >> To: <a moz-do-not-send="true"
class="ecxmoz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> Subject: Re: [gmx-users] simulation killed<br>
> ><br>
> >><br>
> >> something killed your job but it wasn't
gromacs.<br>
> >> Your system has run time or memory
requirements that your job exceeded.<br>
> >><br>
> >> On 2012-01-29 06:40:29PM +0200, mehmet
kıytak wrote:<br>
> >> > hi! all<br>
> >> ><br>
> >> > ı have to a big problem..ı am doing
free energy calculation for a ligand<br>
> >> > (L<br>
> >> > histidine ) when ı perform mdrun ..
my simulation stop ... the program<br>
> >> > gave<br>
> >> > me this message..<br>
> >> ><br>
> >> > Reading file md0.tpr, VERSION 4.5.4
(single precision)<br>
> >> > Starting 8 threads<br>
> >> > Making 1D domain decomposition 8 x 1
x 1<br>
> > & gt; > starting mdrun 'Protein in
water'<br>
> ><br>
> >> > 2500000 steps, 5000.0 ps.<br>
> >> > ./job_0.sh: line 95: 15457 Killed
mdrun -nt 8 -deffnm<br>
> >> > md$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
moz-do-not-send="true"
class="ecxmoz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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> >> > Can't post? Read <a
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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 moz-do-not-send="true"
class="ecxmoz-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
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class="ecxmoz-txt-link-abbreviated"
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> >> <a moz-do-not-send="true"
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> ><br>
> > --<br>
> > gmx-users mailing list <a
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