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[weixin]

Is your simulation box (20*20*20 A^3) big enough?




2008/4/7 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
> P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
>
>
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