[gmx-users] Question regarding rebuilding the simulation box

[Mark Abraham]

Hi,

1 edition
2 yes, but you must adjust the atom count in the file, and be gentle when
reequilibrating

Mark

On Tue, 7 Mar 2017 21:47 <ali.khourshaei71 at student.sharif.edu> wrote:

> Dear gromacs user,
>
> I have 2 question regarding the building of the simulation box from an
> initial configuration.
>
> 1. I have a rectangular box ( 6.45 * 5.35 * 7 ). How can I build a new
> simulation box, containing these atom but in a cubic manner ( 7 * 7 * 7
> )
>
> 2. If I delete some water molecules from an initial configuration by
> omitting these molecules manually from the .gro file, is this valid ?
>
> Sincerely,
>
> Ali
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