[gmx-users] how can we include excluded atoms

[Justin Lemkul]

On 8/7/19 3:21 AM, Anjali Patel wrote:
> Hello user,
>
> i have gone through the manual and according to that all atoms are bonded.
> still its showing non-bonded parameters with excluded atoms. due to this
> its showing error like this,
>
> Excluding 1 bonded neighbours molecule type 'NP5Q'

This is incorrect. nrexcl should be 3 for all molecules. This is the 
force field convention for basically all biomolecular force fields. 1-2 
and 1-3 nonbonded interactions are never calculated.

> Excluding 3 bonded neighbours molecule type 'DRG'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> WARNING 1 [file topol.top, line 60]:
>    The GROMOS force fields have been parametrized with a physically
>    incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>    used with a single-range cut-off (or a correct Trotter
>    multiple-time-stepping scheme), physical properties, such as the density,
>    might differ from the intended values. Check if molecules in your system
>    are affected by such issues before proceeding. Further information may be
>    available at https://redmine.gromacs.org/issues/2884.

Heed this warning.

> Fatal error:
> number of coordinates in coordinate file (solv.gro, 3789)
>               does not match topology (topol.top, 3777)

The error means you're not doing your bookkeeping correctly, but this 
has nothing to do with the exclusions listed above, which are part of 
the physical form of the simulation.

-Justin

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Justin A. Lemkul, Ph.D.
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