[gmx-users] Flat-bottomed Restrain

[Mark Abraham]

Hi,

On Tue., 16 Jul. 2019, 10:32 ehsan shahini, <ehsan.shahiny at gmail.com> wrote:

> Dear all,
>
> 1. I need to restrain a small molecule in a region (cylindrical) and I want
> to restrain all of its atoms in that region. The best tool is flat-bottomed
> restrain but it only restrains individual atoms in their corresponding
> regions and not all the atoms in a single region.
>
> Hence, if I want to change the main code related to flat-bottomed where can
> I find it?
>

No need. Use grompp -r to restrain the position of each atom to the same
position that is the centre of the desired region.

Another question
>
> 2. Can we introduce virtual sites in Gromacs which are static and defined
> by the user via the XYZ coordinates of them?
>

No, but you can have frozen particles that have whatever interactions that
you choose.

Mark


Kind regards,
>
> Ehsan
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