[gmx-users] Question regarding rebuilding the simulation box

[Mark Abraham]

Hi,

I don't see any problem, nor how I can guess what mdrun was complaining
about. :-)

Mark

On Wed, 8 Mar 2017 00:13 <ali.khourshaei71 at student.sharif.edu> wrote:

> Dear Mark,
>
> Thanks for your response. Actually, my simulation box contains polarize
> water + lipid. So, when I exert editconf on it, it consider the
> particles of each water molecules ( wp p wm) as separate molecules and
> then  when I want to do mdrun it gives me an error to revise my
> system.top . But I know that this shouldn't happen.
>
> I used :
>
> editconf -f Input.gro -bt cubic  -o Input2.gro -p system.top
>
> At first in Input.gro:
>
> 1041W        W 2449   2.572   2.578   7.383
> 1041W       WP 2449   2.632   2.668   7.473
> 1041W       WM 2449   2.702   2.738   7.573
>
> But, in Input2.gro :
>
> 1041W        W 4273   2.572   2.578   7.383
> 1041W       WP 4274   2.632   2.668   7.473
> 1041W       WM 4275   2.702   2.738   7.573
>
> Sincerely,
>
> Ali
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