[gmx-users] Regarding index .ndx files

Sebastian Muraru sebastian.muraru at grabtop.upb.ro
Mon Sep 17 12:58:09 CEST 2018

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?


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