[gmx-users] (no subject)

[Mahnam]

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/
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