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

ZHANG Cheng 272699575 at qq.com
Wed Dec 6 14:48:33 CET 2017

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, ... ?

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, ..., ?

Thank you.


------------------ Original ------------------
From:  "Mark Abraham";<mark.j.abraham at gmail.com>;
Date:  Wed, Dec 6, 2017 04:34 AM
To:  "gmx-users"<gmx-users at gromacs.org>;
Cc:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>; "ZHANG Cheng"<272699575 at qq.com>; 
Subject:  Re: [gmx-users] How the index is recognised for values more than 99999?

The numbering of the coordinate file is not significant for this, precisely for that reason.
On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699575 at qq.com> wrote:

Dear Gromacs,I am doing the RMSD calculation for a particular group of protein residues. My system also has water molecules so there are more than 99999 atoms. Thus, the 100000th atom is indexed as 0, and 100001th atom as 1, and so on.
 So if the index file for my group has an entry of 1, how can the gromacs know it is the 1st atom, instead of the 100001th atom?
 Thank you.
 Yours sincerely
 Gromacs Users mailing list
 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list