[gmx-users] mix solvent

Mahnam mahnam at ibb.ut.ac.ir
Tue Apr 8 16:24:00 CEST 2008

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

Can not read/write topologies to file type mdp

attached  the mdp  file for position restrain step to this mail.
whould you  please guide my for solving this poblem.  

thanks in  advance for your help and your reply.
 Yours truly 
  Institute of Biochemistry  and Biophysics (IBB)
Tehran     University
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