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 -- ================================================== 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.
