[gmx-users] Range Checking error

[Gaurav Chopra]

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>)
/>/ -------------------------------------------------------
/>/ 
/>/ _______________________________________________
/>/ gmx-users mailing list    gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
/>/ http://www.gromacs.org/mailman/listinfo/gmx-users
/>/ Please don't post (un)subscribe requests to the list. Use the www 
/>/ interface or send it to gmx-users-request at gromacs.org. <http://www.gromacs.org/mailman/listinfo/gmx-users>
/>/ Can't post? Read http://www.gromacs.org/mailing_lists/users.php
/

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++