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Dear Rui,<br>
<br>
Thanks for the info - maybe it's better to submit a bugzilla for the
NMA in parallel then, do I'm not sure if this can be checked on
run-time with mdrun. From Nahren's description I understood that
multiples files were generated and assumed that they were backups (as
if you run identical MD multiple times with the same input and files).<br>
<br>
Ran<br>
<br>
J. Rui Rodrigues wrote:
<blockquote cite="mid20100728121324.M63222@estg.ipleiria.pt" type="cite">
<pre wrap="">Dear Ran and Nahren,
I run into a similar problem a couple of weeks ago:
<a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/2010-July/052377.html">http://lists.gromacs.org/pipermail/gmx-users/2010-July/052377.html</a>
In short,
"integrator = steep " can be run in parallel. Output from parallel and
single-node are equal.
"integrator = l-bfgs" runs only in single-node, as advertised in the
manual. mdrun dies with a fatal error if one tries to run in parallel:
Fatal error: Cannot do parallel L-BFGS Minimization - yet.
"integrator = nm" runs in parallel without any error. However, output
is wrong: mdrun write multiple hessian.mtx files, each with small size.
mdrun seems to get in to some kind of race condition, because sometimes
only one .mtx is produced (still, with small size). Running g_nmeig in these
"parallel" mtx results in huge all-negative eigenvalues.
The same input in single-node goes just fine, with first 6 eigenvalues close
to zero.
Rui Rodrigues
On Wed, 28 Jul 2010 12:55:44 +0200, Ran Friedman wrote
</pre>
<blockquote type="cite">
<pre wrap="">Your NMA seem to run on one processor four times. I'm not sure if the EM
part can be run in parallel. This doesn't seem to be the reason for the
negative eigenvalue. What was the g_anaeig command (with flags)?
nahren manuel wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Ran,
I ran the whole NMA again and I found where I go wrong. I hope it will
help others as well.
(sorry for a big email)
In steps 1 & 2 (of minimization) I kept the C-alpha frozen.
1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr
Steepest Descents converged to Fmax < 100 in 2569 steps
Potential Energy = -6.21296128286120e+03
Maximum force = 9.87358378592302e+01 on atom 701
Norm of force = 1.04875323563923e+01
2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t
em1tpr.trr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr
Polak-Ribiere Conjugate Gradients converged to Fmax < 1 in 6596 steps
Potential Energy = -7.56682084795001e+03
Maximum force = 9.92719787231560e-01 on atom 1320
Norm of force = 6.47772253797808e-02
3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t
em2tpr.trr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 3018 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -8.49398064549505e+03
Maximum force = 6.86336687926682e+01 on atom 935
Norm of force = 7.15798864024085e+00
4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t
em3tpr.trr
mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 0.01
writing lowest energy coordinates.
Polak-Ribiere Conjugate Gradients converged to machine precision in
21674 steps,
but did not reach the requested Fmax < 0.01.
Potential Energy = -9.66058047638671e+03
Maximum force = 1.49342602818840e+00 on atom 590
Norm of force = 1.86576579430541e-01
5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t
em4tpr.trr
~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr
Low-Memory BFGS Minimizer converged to machine precision in 10346 steps,
but did not reach the requested Fmax < 0.0001.
Potential Energy = -9.66337416273684e+03
Maximum force = 6.48625019025464e-04 on atom 581
Norm of force = 6.35632681200205e-05
6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t
em5tpr.trr
Low-Memory BFGS Minimizer converged to machine precision in 3316 steps,
but did not reach the requested Fmax < 1e-08.
Potential Energy = -9.66337416275038e+03
Maximum force = 6.48788529801368e-05 on atom 8
Norm of force = 6.56362137550289e-06
7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t
em6tpr.trr
Low-Memory BFGS Minimizer converged to machine precision in 7530 steps,
but did not reach the requested Fmax < 1e-08.
Potential Energy = -9.66337416275071e+03
Maximum force = 4.07762128402886e-07 on atom 10
Norm of force = 5.79534451487287e-08
8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t
em7tpr.trr
Low-Memory BFGS Minimizer converged to Fmax < 1e-08 in 5840 steps
Potential Energy = -9.66337416275070e+03
Maximum force = 8.41750710592449e-09 on atom 521
Norm of force = 1.28889193955553e-09
NMA
9. doublegrompp -f nma.mdp -t em8tpr.trr -c em8tpr.gro -p r1top.top -o
nmatpr.tpr
~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr
(a sinlge processor)
~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr
it created only one nmatpr.mtx
Maximum force: 8.41751e-09
Finished step 1400 out of 1400
It creates the output nmatpr.mtx nmatpr.edr etc....
Now I delete all nma files
rm nmatpr.*
(4 processor)
mpirun -np 4 ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr
Maximum force: 8.41768e-09
Maximum force: 8.41768e-09
Maximum force: 8.41768e-09
Maximum force: 8.41768e-09
Finished step 1399 out of 1400
Writing Hessian...
Writing Hessian...
Writing Hessian...
Finished step 1400 out of 1400
Writing Hessian...
Back Off! I just backed up nmatpr.mtx to ./#nmatpr.mtx.2#
It gives me negative eigenvalues.
One would expect it should not create nmatpr.mtx.1 nmatpr.mtc.2
etc...since these files have been removed. Because it created multiple
nmatpr.mtx file and backup one over another
I am not sure If the problem occurs with my system , but other MPIRUN
(with mdrun) do not create such backup.
Best,
nahren
--- On *Wed, 7/28/10, Ran Friedman /<a class="moz-txt-link-rfc2396E" href="mailto:r.friedman@bioc.uzh.ch"><r.friedman@bioc.uzh.ch></a>/* wrote:
From: Ran Friedman <a class="moz-txt-link-rfc2396E" href="mailto:r.friedman@bioc.uzh.ch"><r.friedman@bioc.uzh.ch></a>
Subject: Re: [gmx-users] Entropy from NMA
To: "Discussion list for GROMACS users" <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Date: Wednesday, July 28, 2010, 3:10 PM
p.s. How big is this negative value?
Ran Friedman wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> Hi,
Can you post the exact commands you used for EM and NMA?
Ran
nahren manuel wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> Dear Gromacs Users,
I am trying to calculate Entropy from Normal Mode Analysis.
I minimized the structure to
8.41750710592449e-09
Then I calculated the normal mode (the mdp file is given below).
But when i try to calculate the Eigenvalues, I get the following
warning
One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...
I get only negative eigenvalues.
Let me also add that I used the same mdp file for minimization
changing the integrator to steep, cg and finally to l-bfgs.
Best,
nahren
-----------------------
integrator = nm
constraints = none
define = -DFLEXIBLE
emtol = 0.00000001
emstep = 0.00000001
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.5
coulombtype = shift
rcoulomb-switch = 1.0
rvdw-switch = 1.0
vdwtype = shift
rcoulomb = 1.3
rvdw = 1.3
</pre>
</blockquote>
<pre wrap="">
--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a> <a class="moz-txt-link-rfc2396E" href="mailto:/mc/compose?to=r.friedman@bioc.uzh.ch"></mc/compose?to=r.friedman@bioc.uzh.ch></a>
Skype: ran.friedman
------------------------------------------------------
</pre>
</blockquote>
<pre wrap="">
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</pre>
</blockquote>
<pre wrap="">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
</blockquote>
<pre wrap=""><!---->
--
Webmail ESTG de Leiria (<a class="moz-txt-link-freetext" href="http://webmail.estg.ipleiria.pt">http://webmail.estg.ipleiria.pt</a>)
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
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