[gmx-users] Regarding index .ndx files

[Kevin Boyd]

Hi!

There are two key points here.

1) Index groups don't have to be mutually exclusive. So, you can have your
20+ indices, but also have an inclusive index that encompasses more or all
of your atoms, which you can then use for tc (or comm removal, etc.). The
only necessary thing is that the indices specified in tc-groups are
complete and exclusive.

2) Gromacs by default does just this - the "system" index Vytautas
mentioned is typically autogenerated and contains every atom in your
system. However, you should see if this is the correct option for you. A
lot of protocols e.g. couple protein separate from the solvent - your
initial setup seems to do something like this. If the only other particles
in your system are solvent, and you have an SOL index, you can just add
that column to your original setup. You might also have ions in your system
- these should be coupled in the same group as the solvent.

Kevin

On Mon, Sep 17, 2018 at 7:14 AM, Vytautas Rakeviius <vytautas1987 at yahoo.com>
wrote:

>  Without going into details and setting:
> tc-grps = System
> should allow to proceed without fatal errors.
>     On Monday, September 17, 2018, 1:58:50 PM GMT+3, Sebastian Muraru <
> sebastian.muraru at grabtop.upb.ro> wrote:
>
>  Hi there! I am a Masters student and this is my first email to the list.
> I would just like to ask whether someone can clarify something for me
> regarding the index .ndx files.
> I am using an nvt.mdp file in order to run an nvt equilibration step. The
> section of interest is the following (currently receiving an error):
>
> ###
> ; Temperature coupling is on
> tcoupl          = V-rescale                ; modified Berendsen thermostat
> tc-grps        = CX ssdna; two coupling groups - more accurate
> tau_t          = 0.1    0.1    ; time constant, in ps
> ref_t          = 300    300    ; reference temperature, one for each
> group, in K
> ###
>
> The current error says that a number of atoms are not part of any of the
> T-Coupling groups. Therefore I have the following questions:
> - Does this mean all atoms (including SOL) must be included in the groups
> specified using 'tc-grps'?
> - If my index.ndx file is very large (contains > 20 groups), do I have to
> manually write them down at 'tc-grps' in the mdp file or is there a way to
> automatically import the groups present in the index.ndx file?
>
> Best,
> Sebastian
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