[gmx-users] Energy minimization Error
francesca vitalini
francesca.vitalini11 at gmail.com
Fri Feb 10 18:15:25 CET 2012
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
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:-) 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 at 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?
Thanks
Fra
2012/2/10 francesca vitalini <francesca.vitalini11 at 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.Abraham at 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. It should have been within [ 0 ..
>> 27744 ]
>> Please report this to the mailing list (gmx-users at 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 <jalemkul at 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 | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> --
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>>>
>>
>>
>>
>> --
>> Francesca Vitalini
>>
>> PhD student at Computational Molecular Biology Group,
>> Department of Mathematics and Informatics, FU-Berlin
>> Arnimallee 6 14195 Berlin
>>
>> vitalini at zedat.fu-berlin.de
>> francesca.vitalini at fu-berlin.de
>>
>> +49 3083875776
>> +49 3083875412
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Francesca Vitalini
>
> PhD student at Computational Molecular Biology Group,
> Department of Mathematics and Informatics, FU-Berlin
> Arnimallee 6 14195 Berlin
>
> vitalini at zedat.fu-berlin.de
> francesca.vitalini at fu-berlin.de
>
> +49 3083875776
> +49 3083875412
>
>
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de
+49 3083875776
+49 3083875412
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