On 11/02/2012 4:15 AM, francesca vitalini wrote:
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
VERSION 3.3.1
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
If you want to redistribute modifications, please consider that
scientific software is very special. Version control is crucial-
bugs must be traceable. We will be happy to consider code for
inclusion in the official distribution, but derived work must not
be called official GROMACS. Details are found in the README & COPYING
files.
:-) gaia30 (-:
Option Filename Type Description
------------------------------------------------------------
-s EM3.tpr Input Generic run input: tpr tpb tpa xml
-o EM3.trr Output Full precision trajectory: trr trj
-x EM3.xtc Output, Opt! Compressed trajectory (portable xdr
format)
-c EM3.gro Output Generic structure: gro g96 pdb xml
-e EM3.edr Output Generic energy: edr ene
-g EM3.log Output Log file
-dgdl EM3.xvg Output, Opt. xvgr/xmgr file
-field EM3.xvg Output, Opt. xvgr/xmgr file
-table EM3.xvg Input, Opt. xvgr/xmgr file
-tablep EM3.xvg Input, Opt. xvgr/xmgr file
-rerun EM3.trr Input, Opt. Generic trajectory: xtc trr trj gro
g96 pdb
-tpi EM3.xvg Output, Opt. xvgr/xmgr file
-ei EM3.edi Input, Opt. ED sampling input
-eo EM3.edo Output, Opt. ED sampling output
-j EM3.gct Input, Opt. General coupling stuff
-jo EM3.gct Output, Opt. General coupling stuff
-ffout EM3.xvg Output, Opt. xvgr/xmgr file
-devout EM3.xvg Output, Opt. xvgr/xmgr file
-runav EM3.xvg Output, Opt. xvgr/xmgr file
-pi EM3.ppa Input, Opt. Pull parameters
-po EM3.ppa Output, Opt. Pull parameters
-pd EM3.pdo Output, Opt. Pull data output
-pn EM3.ndx Input, Opt. Index file
-mtx EM3.mtx Output, Opt. Hessian matrix
-dn EM3.ndx Output, Opt. Index file
-coarse ION.gro Input Generic trajectory: xtc trr trj gro
g96 pdb
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string EM3 Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the
output
xvg files for the xmgrace program
-np int 1 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate
a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an
X-Ray
bombardment on your system
Back Off! I just backed up EM3.log to ./#EM3.log.2#
Getting Loaded...
Reading file EM3.tpr, VERSION 3.3.1 (single precision)
Loaded with Money
Back Off! I just backed up EM3.edr to ./#EM3.edr.2#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 200
------------------------------------------------------- inf,
atom= 15321
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 ..
42875 ]
Please report this to the mailing list (gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>)
-------------------------------------------------------
"With a Lead Filled Snowshoe" (F. Zappa)
Halting program mdrun
gcq#159: "With a Lead Filled Snowshoe" (F. Zappa)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
So... How ca I overcome the issue of overlapping atoms?
Generate better FG structures using a better method.
Try vacuum MD or SA with tiny time steps and no bond constraints.
Mark
Thanks
Fra
2012/2/10 francesca vitalini <francesca.vitalin...@gmail.com
<mailto:francesca.vitalin...@gmail.com>>
In fact in the reverse transformation I'm feeding the CG structure
information.
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.
What do you think?
2012/2/10 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 11/02/2012 12:41 AM, francesca vitalini wrote:
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.
Getting Loaded...
Reading file EM1-1.tpr, VERSION 3.3.1 (single precision)
Loaded with Money
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 2000
------------------------------------------------------- inf,
atom= 15300
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each
particle to a grid
based on its coordinates. If your system contains collisions
or parameter
errors that give particles very high velocities you might end
up with some
coordinates being +-Infinity or NaN (not-a-number).
Obviously, we cannot
put these on a grid, so this is usually where we detect those
errors.
Make sure your system is properly energy-minimized and that
the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648 <tel:2147483648>. It should
have been within [ 0 .. 27744 ]
Please report this to the mailing list (gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>)
-------------------------------------------------------
"Oh My God ! It's the Funky Shit" (Beastie Boys)
Halting program mdrun
You suggested to check if there is any overlapping.
... so you need to get out some visualization software and
look at the transformed structure :)
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.
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.
Mark
Any ideas?
Thanks.
Francesca
2012/2/10 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>>
francesca vitalini wrote:
I achieve
Steepest Descents converged to machine precision in
205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom
1520 (parto of the protein)
Norm of force = 2.28369808518165e+06
The magnitude of the force suggests atomic overlap
somewhere. Start by investigating the environment around
atom 1520.
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
The "step.pdb" files are written when mdrun is about to
crash.
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
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.
Steepest Descents converged to machine precision in
72 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.0135496e+07
Maximum force = 2.0486184e+12 on atom 4479
Norm of force = 7.2424045e+13
Again, symptomatic of severe atomic overlap.
but again the same issue with table extent and still
the production of pdb files.
Any explanations?
Investigate the starting configurations near the
problematic atoms.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Francesca Vitalini
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Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
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Francesca Vitalini
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Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
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Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vital...@zedat.fu-berlin.de <mailto:vital...@zedat.fu-berlin.de>
francesca.vital...@fu-berlin.de <mailto:francesca.vital...@fu-berlin.de>
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