[gmx-users] Regarding energy group exclusion

[Nashit Jalal 17250017]

Dear all,

I have a protein with three chains PROA, PROB and PROC. I want to check
inter interactions of PROA, PROB, PROC and SOL by keeping PROC frozen (not
to include intra interactions). I have changes mdp file using the following
parameters:


nsteps = 50000   ; Maximum number of (minimization) steps to perform
energygrps = PROA PROB PROC SOL ; Which energy group(s) to write to disk
energygrp_excl  = PROA PROA PROB PROB PROC PROC SOL SOL PROA SOL PROB SOL
freezegrps      = PROC
freezedim       = Y Y Y

I have also made these groups in index file.
Still it is giving following error.

error: There were 4 notes

There were 2 warnings

-------------------------------------------------------
Program:     gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)

Fatal error:
There was 1 error in input file(s)

Please guide me on the error and corrections in my method. I have used
-maxwarn and -n index. If I don't use -n index it gave following error:


Fatal error:
Group PROC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.


Thank you,
Nashit