[gmx-users] Regarding index .ndx files

[João Henriques]

What is your system composed of? It is generally a good idea to couple
solvent and solute separately (as long as solute is "big enough", see
http://www.gromacs.org/Documentation/Terminology/Thermostats), so Vytautas
reply isn't the best advice. It will solve your problem, but that's
generally not the way to proceed, and definitely not the most educative.

Regarding the part about index groups, you can group groups into a single
index entry to facilitate things. You can easily create a group with all
things solute and another with solvent + salt. This way you can couple them
separately, assuming that makes sense for your system (you didn't specify
what it is, so it's hard to help a lot more than this).

J

On Mon, Sep 17, 2018 at 1:15 PM 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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