Quoting Mahnam <[EMAIL PROTECTED]>: > In God We Trust > Hello GMX > users > I want to equilibrate my protein in a mix solvent, befor this > work, I made a cubic box that it contained 215 spc water and 5 proline > molecule (without protein) with 20*20*20 angestrom and then I minimized > it. when I do position restrain with NPT ensemble and pressure coupling > (for 20 ps) for this box, and the box size increase and big holes are > created in the box. Also I > can do MD at 100 K after this step, but MD at 200 K is imposible and it > says : > > Grid: 25 x 25 x 25 cells > WARNING: your box is exploding! > (ncells = 15625)
You have probably generated some severe atomic overlap. How did you prepare your system? Command line input would be useful here. Did steepest descents converge to an appropriate potential energy? Have a look here for some general advice: http://wiki.gromacs.org/index.php/blowing_up > > ------------------------------------------------------- > Program mdrun, > VERSION 3.3.1 > Source code file: gmxfio.c, line: 784 > > Fatal > error: > Can not read/write topologies to file type mdp What was the exact command line you issued when executing mdrun? -Justin > > I > attached the mdp file for position restrain step to this mail. > > whould you please guide my for solving this poblem. > > Many > thanks in advance for your help and your reply. > Yours truly > Karim > Mahnam > Institute of Biochemistry and Biophysics (IBB) > Tehran > University > P.O.box 13145-1384 > Tehran > Iran > > http://www.ibb.ut.ac.ir/ > ======================================== 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 gmx-users@gromacs.org 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
