[gmx-users] defining parameters in a separate itp file

[Justin Lemkul]

On 10/28/19 6:21 PM, Dave M wrote:
> Hi Justin,
>
> Thanks for your reply but am getting error suggesting a intermolecular
> chemical bond is not allowed:
>
> Program:     gmx grompp, version 2016.4
>
> Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)
>
> Fatal error:
>
> The intermolecular_interaction can not contain chemically bonding
> interactions
>
> [ molecules ]
>
> ; name        number
>
> molA 1
>
> molB 1
>
> W  2420
>
>
> [intermolecular_interactions]
>
>   [ bonds ]
>
>      1     158     1  0.4  2000
>
> This is coarse-grained model and as a simple test I used global atom
> numbers between two water single particles (intermolecular) but I get the
> same error.

In that case, use a [distance_restraints] directive under 
[intermolecular_interactions] (though this will limit your domain 
decomposition setup) or use the pull code to maintain a restraint rather 
than messing with the topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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