[gmx-users] atom indexing in top and gro files

[Justin Lemkul]

On 11/27/19 8:56 PM, Ling Chan wrote:
> Dear Justin,
>
> Many thanks for your quick reply! I really appreciate it.
>
>
>    *   The code requires all [moleculetype] directives to be numbered from 1. This has no relationship to the actual global atom numbers in the coordinate file. What must be true is that the atoms in the topology and coordinate files appear in the same order.
>
> I would just to confirm that the following is correct. All the atomic indices referred to in the “bonds” “angles” “dihedrals” blocks are in fact the line number of the atoms. They are not related to the “atom index” . In other words, if there are 78 lines in the “atoms” block, the following would be an invalid entry in the “bonds” block even if one of my atoms has an index “95”.
> [bonds]
>    69  95  1

The only valid numbers are {1..N}, which are entirely defined by [atoms] 
within the [moleculetype]. You will get an obvious error message from 
grompp if you don't satisfy this requirement.

-Justin

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Justin A. Lemkul, Ph.D.
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