There is a default index group for the whole system, 9 default index groups for proteins, and a default index group is generated for every other residue name.
When no index file is supplied, also gmx makendx will generate the default groups. This page no longer contains the latest GROMACS documentation. Please update your bookmarks, and see Here are Gromacs users: I am studying a peptide interacting with a protein using the gmx Hbond command. I want to make an index (makendx) file for a. tpr and select a residue in the peptide. I cannot The GROMACS index file (usually called index. ndx) contains some user definable sets of atoms.
The file can be read by most analysis programs, by the graphics program and by the preprocessor. Most of these programs create default index groups when no index file is supplied, so you only need to make an index file when you need special groups.
Gromacs input preparation 1. Process the pdb file with pdb2gmx The pdb2gmx command converts your pdb file to a gromacs file and writes the topology for you. This file is derived from an NMR structure which contains hydrogen atoms. Therefore, we use theignh flag to ignore hydrogen atoms in the pdb file. Manual and GROMACS versions We try to release an updated version of the manual whenever we release a new version of the soft ware, so in general it is a good idea to use a manual with the same major and minor release number NAME gromacs molecular dynamics simulation suite CONTENTS DESCRIPTION GROMACS (the Groningen Machine for Chemical Simulations) is a fullfeatured suite of programs to perform molecular dynamics simulations in other words, to simulate the behavior of systems with hundreds to millions of particles, using Newtonian equations This manual page is largely based on the GROMACS online reference, and was prepared in this format by Nicholas Breen.
BUGS GROMACS has no major known bugs, but be warned that it stresses your CPU more than most software. GROMACS Introductory Tutorial Gromacs ver 4. 5 Author: John E. Kerrigan, Ph. D. Associate Director, Bioinformatics command converts your pdb file to a gromacs file and writes the topology for you. This file is (please see the Gromacs user manual for more information).