[gmx-users] How the index is recognised for values more than 99999?
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 9 atoms. Thus, the 10th atom is indexed as 0, and 11th 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 11th atom? Thank you. Yours sincerely Cheng -- 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-requ...@gromacs.org.
Re: [gmx-users] How the index is recognised for values more than 99999?
Hi, The numbering of the coordinate file is not significant for this, precisely for that reason. Mark On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699...@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 > 9 atoms. Thus, the 10th atom is indexed as 0, and 11th 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 11th atom? > > > Thank you. > > > Yours sincerely > Cheng > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
Re: [gmx-users] How the index is recognised for values more than 99999?
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 11th, 12th, 13th, ... ? 2) And if I want the RMSD for the group containing atom 11th, 12th, 13th, ..., I need to write their indices as 11, 12, 13, ..., ? Thank you. Cheng -- Original -- From: "Mark Abraham";; Date: Wed, Dec 6, 2017 04:34 AM To: "gmx-users"; Cc: "gromacs.org_gmx-users"; "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] How the index is recognised for values more than 9? Hi, The numbering of the coordinate file is not significant for this, precisely for that reason. Mark On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699...@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 9 atoms. Thus, the 10th atom is indexed as 0, and 11th 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 11th atom? Thank you. Yours sincerely Cheng -- 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
Re: [gmx-users] How the index is recognised for values more than 99999?
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 11th, 12th, 13th, ... ? Yes. GROMACS does what you tell it. If you want atom 1, use 1. If you want atom 11, use 11. 2) And if I want the RMSD for the group containing atom 11th, 12th, 13th, ..., I need to write their indices as 11, 12, 13, ..., ? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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-requ...@gromacs.org.
