[gmx-users] mix solvent

[Justin A. Lemkul]

I gave you advice:

http://www.gromacs.org/pipermail/gmx-users/2008-April/033307.html

So what have you done to help yourself?  Asking the same question without
demonstrating that you've attempted to respond to the advice given will surely
get you nowhere.

-Justin

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)
>
> -------------------------------------------------------
> 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
>



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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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