<html><head><style type="text/css"><!-- DIV {margin:0px} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>you may check your model it may severely distorted.<br><br>Yang Ye<br><br>----- Original Message ----<br>From: hnam <mahnam@ibb.ut.ac.ir><br>To: gmx-users@gromacs.org<br>Sent: Wednesday, January 04, 2006 7:20:00 PM<br>Subject: [gmx-users] mdrun problem<br><br> <div><br>In the name of God</div> <div>Hello everyone </div> <div>i constraint one water molecule in active site my protein.</div> <div>When I run mdrun with md.mdp ,it says:</div> <div>Program mdrun, VERSION 3.3<br>Source code file: nsgrid.c, line: 226</div> <div>Range checking error:<br>Explanation: During neighbor searching, we assign each particle to a grid<br>based on its coordinates. If your system contains collisions or parameter<br>errors that give particles ve
ry high velocities you might end up with some<br>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>put these on a grid, so this is usually where we detect those errors.<br>Make sure your system is properly energy-minimized and that the potential<br>energy seems reasonable before trying again.</div> <div><strong>Variable ci has value -2147483648. It should have been within [ 0 .. 2744 ]<br>Please report this to the mailing list</strong> (<a target="_blank" id="bodyLinks" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>)</div> <div>Would you please tell me what it means.<br>Thank you very much in advance<br>Institute of Biochemistry and Biophysics (IBB)<br>Tehran University <br>P.O.box 1417614411<br>Tehran <br>Iran <br><br> </div> <div>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br><a target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-use
rs">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.</div></div></div></div></body></html>