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
prmd-npt.mdp
Description: Binary data
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