[gmx-users] Regarding energy group exclusion

[Justin Lemkul]

On 12/27/19 6:30 AM, Nashit Jalal 17250017 wrote:
> 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:

Don't use -maxwarn to circumvent errors. If you need help with the 
actual errors, you need to provide us with the actual text of those errors.

If you simply want to analyze interaction energy between two species 
from an existing simulation, you don't need any of the above, you just 
need "energygrps = PROA PROB"

-Justin

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Justin A. Lemkul, Ph.D.
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