Gaurav Chopra wrote:
/ Hi
/>/
/>/ I am doing a steepest descent for the initial mdrun for a peptide and it
/>/ gives me the following error. Please advice.
/>/
/>/ Thanks
/>/ Gaurav
/>/ -------------------------------------------------------
/>/ Program mdrun, VERSION 3.3
/>/ 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.
/Please follow the advice in the above two sentences. Check your structure.
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
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.
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
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:
also segmentation fault.
Is there a different method to do energy minimization better as suggested in
the range check error warning.
Thanks
Gaurav
/
/>/ Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
/>/ Please report this to the mailing list (gmx-users at gromacs.org
<http://www.gromacs.org/mailman/listinfo/gmx-users>)
/>/ -------------------------------------------------------
/>/
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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
spoel at xray.bmc.uu.se <http://www.gromacs.org/mailman/listinfo/gmx-users>
spoel at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
http://folding.bmc.uu.se
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