[gmx-users] (no subject)

[Justin A. Lemkul]

Quoting Mahnam <mahnam at ibb.ut.ac.ir>:

> 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)

You have probably generated some severe atomic overlap.  How did you prepare
your system?  Command line input would be useful here.  Did steepest descents
converge to an appropriate potential energy?  Have a look here for some general
advice:

http://wiki.gromacs.org/index.php/blowing_up

>
> -------------------------------------------------------
> Program mdrun,
> VERSION 3.3.1
> Source code file: gmxfio.c, line: 784
>
> Fatal
> error:
> Can not read/write topologies to file type mdp

What was the exact command line you issued when executing mdrun?

-Justin

>
> 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/
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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