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<pre>Gaurav Chopra wrote:
><i> Hi
</i>><i>
</i>><i> I am doing a steepest descent for the initial mdrun for a peptide and it
</i>><i> gives me the following error. Please advice.
</i>><i>
</i>><i> Thanks
</i>><i> Gaurav
</i>><i> -------------------------------------------------------
</i>><i> Program mdrun, VERSION 3.3
</i>><i> Source code file: nsgrid.c, line: 226
</i>><i>
</i>><i> Range checking error:
</i>><i> Explanation: During neighborsearching, we assign each particle to a grid
</i>><i> based on its coordinates. If your system contains collisions or parameter
</i>><i> errors that give particles very high velocities you might end up with some
</i>><i> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
</i>><i> put these on a grid, so this is usually where we detect those errors.
</i>><i> Make sure your system is properly energy-minimized and that the potential
</i>><i> energy seems reasonable before trying again.
</i>Please follow the advice in the above two sentences. Check your structure.
<big><font color="#000099">I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
<font color="#000000">Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 10000
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.</font>
Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
I get the following</font></big>
<font color="#000099"><big><font color="#000000">Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.000000 (between atoms 655 and 657) rms 40665803128832.000000
bonds that rotated more than 30 degrees:</font>
also segmentation fault.
Is there a different method to do energy minimization better as suggested in the range check error warning.
Thanks
Gaurav
</big></font>
><i>
</i>><i> Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
</i>><i> Please report this to the mailing list (<a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">gmx-users at gromacs.org</a>)
</i>><i> -------------------------------------------------------
</i>><i>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,         75124 Uppsala, Sweden
phone:        46 18 471 4205                fax: 46 18 511 755
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">spoel at xray.bmc.uu.se</a>        <a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">spoel at gromacs.org</a> <a
href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a>
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