[gmx-users] How the index is recognised for values more than 99999?

[Justin Lemkul]

On 12/6/17 8:48 AM, ZHANG Cheng wrote:
> Hi Mark,
> I only calculate the RMSD for a particular group. So I need to use a index file, which explicitly indicates the atom indices within that group.
>
>
> 1) So if that group indices contain "1 2 3 ...", the Gromacs software will always assume they are 1st, 2nd, 3rd, ... atoms, instead of 100001th, 100002th, 100003th, ... ?

Yes. GROMACS does what you tell it. If you want atom 1, use 1. If you 
want atom 100001, use 100001.

>
> 2) And if I want the RMSD for the group containing atom 100001th, 100002th, 100003th, ..., I need to write their indices as 100001, 100002, 100003, ..., ?
>

Yes.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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