Quoting mahendra awale <[EMAIL PROTECTED]>: > hi > > dear sir > > i am mahendra awale doing M.S in NIPER INDIA in pharmacoinformatics > i am running MD simulation > i have a problem while running MD would u please help me
It is best to keep Gromacs-related questions on the users' list, and I am copying the other members so that an archived copy of this message will be preserved for others to use. Please send questions to the gmx-users list in the future. You also have a much better chance of reaching someone who knows how to solve your problem. See below for my ideas on your situation. > > 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. It is hard to say what might be the problem, but it appears that mdrun has already told you. What step is this - minimization, equilibration, or production? Did you minimize and/or equilibrate your system, and if yes, then how? What is in your system - a simple protein, or some sort of complex system? Without this information, you will likely get no useful help. Check the gmx-users archive for similar problems. This particular issue has been discussed dozens of times in recent memory. Also consult the wiki site (wiki.gromacs.org), specifically: http://wiki.gromacs.org/index.php/Beginners http://wiki.gromacs.org/index.php/Blowing_Up If you need further help, it will be useful to send the message to the gmx-users list, and include: 1. What your system contains 2. How you have minimized or equilibrated your system 3. The text of your .mdp file -Justin > > thank u > > looking forward for u r reply > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
