Is your simulation box (20*20*20 A^3) big enough?
2008/4/7 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) > ------------------------------------------------------- > Program mdrun, VERSION 3.3.1 > Source code file: gmxfio.c, line: 784 > > *Fatal error: > Can not read/write topologies to file type mdp* > > 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/ > > > _______________________________________________ > 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 >
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