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On 11/02/2012 4:15 AM, francesca vitalini wrote:
<blockquote
cite="mid:CAPRCF+KByUCD91m_yo_+X3MWf0=t8PWOktfd7zuGYY5qo5xn5A@mail.gmail.com"
type="cite">Ok now I have tryied to restart it all and the problem
seems to be that the system has some overlapping. In fact, no
matter what I freeze, water, CA or nothing, I get this error
message<br>
<br>
VERSION 3.3.1 <br>
<br>
This program is free software; you can redistribute it
and/or<br>
modify it under the terms of the GNU General Public
License<br>
as published by the Free Software Foundation; either
version 2<br>
of the License, or (at your option) any later
version.<br>
If you want to redistribute modifications, please consider
that<br>
scientific software is very special. Version control is
crucial-<br>
bugs must be traceable. We will be happy to consider code
for<br>
inclusion in the official distribution, but derived work
must not<br>
be called official GROMACS. Details are found in the README
& COPYING<br>
files.<br>
<br>
:-) gaia30 (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-s EM3.tpr Input Generic run input: tpr tpb tpa
xml<br>
-o EM3.trr Output Full precision trajectory: trr
trj<br>
-x EM3.xtc Output, Opt! Compressed trajectory (portable
xdr format)<br>
-c EM3.gro Output Generic structure: gro g96 pdb
xml<br>
-e EM3.edr Output Generic energy: edr ene<br>
-g EM3.log Output Log file<br>
-dgdl EM3.xvg Output, Opt. xvgr/xmgr file<br>
-field EM3.xvg Output, Opt. xvgr/xmgr file<br>
-table EM3.xvg Input, Opt. xvgr/xmgr file<br>
-tablep EM3.xvg Input, Opt. xvgr/xmgr file<br>
-rerun EM3.trr Input, Opt. Generic trajectory: xtc trr trj
gro g96 pdb<br>
-tpi EM3.xvg Output, Opt. xvgr/xmgr file<br>
-ei EM3.edi Input, Opt. ED sampling input<br>
-eo EM3.edo Output, Opt. ED sampling output<br>
-j EM3.gct Input, Opt. General coupling stuff<br>
-jo EM3.gct Output, Opt. General coupling stuff<br>
-ffout EM3.xvg Output, Opt. xvgr/xmgr file<br>
-devout EM3.xvg Output, Opt. xvgr/xmgr file<br>
-runav EM3.xvg Output, Opt. xvgr/xmgr file<br>
-pi EM3.ppa Input, Opt. Pull parameters<br>
-po EM3.ppa Output, Opt. Pull parameters<br>
-pd EM3.pdo Output, Opt. Pull data output<br>
-pn EM3.ndx Input, Opt. Index file<br>
-mtx EM3.mtx Output, Opt. Hessian matrix<br>
-dn EM3.ndx Output, Opt. Index file<br>
-coarse ION.gro Input Generic trajectory: xtc trr trj
gro g96 pdb<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-nice int 19 Set the nicelevel<br>
-deffnm string EM3 Set the default filename for all file
options<br>
-[no]xvgr bool yes Add specific codes (legends etc.) in
the output<br>
xvg files for the xmgrace program<br>
-np int 1 Number of nodes, must be the same as
used for<br>
grompp<br>
-nt int 1 Number of threads to start on each
node<br>
-[no]v bool yes Be loud and noisy<br>
-[no]compact bool yes Write a compact log file<br>
-[no]sepdvdl bool no Write separate V and dVdl terms for
each<br>
interaction type and node to the log
file(s)<br>
-[no]multi bool no Do multiple simulations in parallel
(only with<br>
-np > 1)<br>
-replex int 0 Attempt replica exchange every # steps<br>
-reseed int -1 Seed for replica exchange, -1 is
generate a seed<br>
-[no]glas bool no Do glass simulation with special long
range<br>
corrections<br>
-[no]ionize bool no Do a simulation including the effect
of an X-Ray<br>
bombardment on your system<br>
<br>
<br>
Back Off! I just backed up EM3.log to ./#EM3.log.2#<br>
Getting Loaded...<br>
Reading file EM3.tpr, VERSION 3.3.1 (single precision)<br>
Loaded with Money<br>
<br>
<br>
Back Off! I just backed up EM3.edr to ./#EM3.edr.2#<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+01<br>
Number of steps = 200<br>
-------------------------------------------------------
inf, atom= 15321<br>
Program mdrun, VERSION 3.3.1<br>
Source code file: nsgrid.c, line: 226<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each particle to
a grid<br>
based on its coordinates. If your system contains collisions or
parameter<br>
errors that give particles very high velocities you might end up
with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we
cannot<br>
put these on a grid, so this is usually where we detect those
errors.<br>
Make sure your system is properly energy-minimized and that the
potential<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -2147483648. It should have been within [ 0
.. 42875 ]<br>
Please report this to the mailing list (<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>)<br>
-------------------------------------------------------<br>
<br>
"With a Lead Filled Snowshoe" (F. Zappa)<br>
<br>
Halting program mdrun<br>
<br>
gcq#159: "With a Lead Filled Snowshoe" (F. Zappa)<br>
<br>
--------------------------------------------------------------------------<br>
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD <br>
with errorcode -1.<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
processes.<br>
You may or may not see output from other processes, depending on<br>
exactly when Open MPI kills them.<br>
<br>
<br>
So... How ca I overcome the issue of overlapping atoms?<br>
</blockquote>
<br>
Generate better FG structures using a better method.<br>
<br>
Try vacuum MD or SA with tiny time steps and no bond constraints.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPRCF+KByUCD91m_yo_+X3MWf0=t8PWOktfd7zuGYY5qo5xn5A@mail.gmail.com"
type="cite">Thanks<br>
Fra<br>
<br>
<div class="gmail_quote">2012/2/10 francesca vitalini <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:francesca.vitalini11@gmail.com">francesca.vitalini11@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">In fact in
the reverse transformation I'm feeding the CG structure
information. <br>
Once I look through VMD to the FG structure I notice that the
backbones are not in planes so definitely I need to run some
minimization there. In the tutorial they were using simulating
annealing, but I don't think I need more than energy
minimization for that.<br>
What do you think?
<div class="HOEnZb">
<div class="h5"><br>
<br>
<br>
<br>
<div class="gmail_quote">2012/2/10 Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>
<div> On 11/02/2012 12:41 AM, francesca vitalini
wrote:
<blockquote type="cite">In order to overcome the
problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want
the structure to be maintained). However, if I
do then I have problems with the energy
minimization as the force on the 15300 is
infinite.<br>
<br>
Getting Loaded...<br>
Reading file EM1-1.tpr, VERSION 3.3.1 (single
precision)<br>
Loaded with Money<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+01<br>
Number of steps = 2000<br>
-------------------------------------------------------
inf, atom= 15300<br>
Program mdrun, VERSION 3.3.1<br>
Source code file: nsgrid.c, line: 226<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we
assign each particle to a grid<br>
based on its coordinates. If your system
contains collisions or parameter<br>
errors that give particles very high
velocities you might end up with some<br>
coordinates being +-Infinity or NaN
(not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where
we detect those errors.<br>
Make sure your system is properly
energy-minimized and that the potential<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -<a
moz-do-not-send="true" href="tel:2147483648"
value="+12147483648" target="_blank">2147483648</a>.
It should have been within [ 0 .. 27744 ]<br>
Please report this to the mailing list (<a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a>)<br>
-------------------------------------------------------<br>
<br>
"Oh My God ! It's the Funky Shit" (Beastie
Boys)<br>
<br>
Halting program mdrun<br>
<br>
You suggested to check if there is any
overlapping.</blockquote>
<br>
</div>
</div>
... so you need to get out some visualization
software and look at the transformed structure :)
<div><br>
<br>
<blockquote type="cite"> There might be as my
structure is obtained through a reverse
transformation from a CG representation. In the
mapping the atoms are positioned randomly in the
bead. Now I'm running some energy minimization
to equilibrate those atoms. I had to solvate the
system after the mapping (couldn't do it before
due to problems with ions)but I haven't
equilibrated it yet and I'm keeping it fixed
which could also be a source of overlapping. <br>
</blockquote>
<br>
</div>
Local minimization with EM cannot in general take a
"random" positioning of the generated atoms and make
it one that will be stable under MD. Some structure
knowledge needs to be build into the reverse
transformation.<span><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
<br>
<blockquote type="cite"> Any ideas?<br>
Thanks.<br>
Francesca<br>
<br>
<br>
<div class="gmail_quote">2012/2/10 Justin A.
Lemkul <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div><br>
<br>
francesca vitalini wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> I achieve<br>
<br>
Steepest Descents converged to machine
precision in 205 steps,<br>
but did not reach the requested Fmax
< 10.<br>
Potential Energy =
-1.49131940478719e+07<br>
Maximum force =
1.09664530279637e+06 on atom 1520
(parto of the protein)<br>
Norm of force =
2.28369808518165e+06<br>
<br>
</blockquote>
<br>
</div>
The magnitude of the force suggests atomic
overlap somewhere. Start by investigating
the environment around atom 1520.
<div><br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> and the
system looked with vmd doesn't look as
if it was exploding. However, I have
warnings about the table extension and
I don't know why but gromacs writes
pdb files sometime. However I thought
that there <br>
</blockquote>
<br>
</div>
The "step.pdb" files are written when
mdrun is about to crash.
<div><br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> might have
been an error in the way I defined the
position restraints, in fact in the
mdp file I hade define = -DEPOSRE
while in the topology I had ifdef
DEFINE_WAT, so it might have moved it
all without fixing the water. So I
tried again and this time I got<br>
<br>
</blockquote>
<br>
</div>
The "define" statements are literal, so be
careful of typos. -DEPOSRE will not work
when the topology calls for -DPOSRES. So
unless you've changed default naming for
"define" statements, you're not going to
get what you expect.
<div> <br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> Steepest
Descents converged to machine
precision in 72 steps,<br>
but did not reach the requested Fmax
< 10.<br>
Potential Energy = -2.0135496e+07<br>
Maximum force = 2.0486184e+12 on
atom 4479<br>
Norm of force = 7.2424045e+13<br>
<br>
</blockquote>
<br>
</div>
Again, symptomatic of severe atomic
overlap.
<div><br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> but again the
same issue with table extent and still
the production of pdb files.<br>
<br>
Any explanations?<br>
<br>
</blockquote>
<br>
</div>
Investigate the starting configurations
near the problematic atoms.<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a><span><font
color="#888888"><br>
<br>
-Justin</font></span>
<div>
<div><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a>
| <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080"
value="+15402319080" target="_blank">(540)
231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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<br>
-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology
Group, <br>
Department of Mathematics and Informatics,
FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
<br>
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href="mailto:vitalini@zedat.fu-berlin.de"
target="_blank">vitalini@zedat.fu-berlin.de</a><br>
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-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group, <br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
<br>
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-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group, <br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
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