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</style></head><body> In God We Trust<br>Hello GMX users<br>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 :<br><br>Grid: 25 x 25 x 25 cells<br>WARNING: your box is
exploding! (ncells = 15625)<br>
-------------------------------------------------------<br>Program mdrun,
VERSION 3.3.1<br>Source code file: gmxfio.c, line: 784<br><br><b>Fatal
error:<br>Can not read/write topologies to file type mdp</b><br><br>I
attached the mdp file for position restrain step to this mail.<br>
whould you please guide my for solving this poblem. <br><br> Many
thanks in advance for your help and your reply.<br> Yours truly <br> Karim
Mahnam<br> Institute of Biochemistry and Biophysics (IBB)<br> Tehran
University <br> P.O.box 13145-1384<br> Tehran <br> Iran <br>
http://www.ibb.ut.ac.ir/<br><br> </body>
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