[gmx-users] how to freeze an arbitrary set of atoms

[Mark Abraham]

Hi,

This is called an index group (see manual) and can be made by hand, or with
gmx make_ndx, or gmx select, in increasing order of powerfulness. :-)

Mark

On Fri, Jun 10, 2016 at 3:26 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> I would like to freeze a subset of protein atoms in my system. Since I
> don’t want to freeze them all, I can’t really do the following:
>
> freezegrps      = Protein-H
> freezedim       = Y Y Y
>
> How can I define a custom set, e.g. atom indices {400,1200,234} etc.?
>
> Best,
> Irem
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