Gromos manual

# The vaiables GROMOS_FILE and ATOMTYPE_FILE has to be specified as required. # The output file requires some manual modifications: # add ACE and NH2 # add 4 dihedrals with parameters 0 0 2 in HEME # remove I in front of all atoms names in SO# make a copy of H2O called HOH # author: Klaas Dijkstra, Univ. Groningen # Oct. The GROMOSsoftware manuals that accompanied the major releases of 19are W.F. van Gunsteren and H.J.C. Berendsen Groningen Molecular Simulation (GROMOS) Library Manual Biomos, Groningen, The Netherlands, , pp. W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H. Hu¨nenberger, P. Kru¨ger, A.E. Mark, W.R.P. Scott and I.G. Tironi. Manual editing of GROMOS topology (EDITOP) The command EDITOP first converts the binary GROMOS topology file (www.doorway.ru) to ASCII format. This ASCII file is then pulled into your favourite editor for manual adjustments. After saving a new binary topology file is generated. Viewing energy files from an MD run (ENERAN).

Reference Manual¶ This part of the documentation covers implementation details of GROMACS. For quick simulation set-up and short explanations, please refer to the User guide. GROMOS is is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. It also incorporates its own force field covering proteins, nucleotides, sugars etc. and can be applied to chemical and physical systems ranging from glasses and liquid crystals, to polymers and crystals and solutions of biomolecules. USER MANUAL Version David van der Spoel, Erik Lindahl, Berk Hess Aldert R. van Buuren Emile Apol Pieter J. Meulenhoff D. Peter Tieleman Alfons L.T.M. Sijbers K. Anton Feenstra Rudi van Drunen Herman J.C. Berendsen c Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, AG Groningen, The Netherlands.

exponential format, the GROMOS programs are independent of the chosen units. The units are defined by the ones used for physical constants (Tab. ) and atomic or molecular quantities in the (GROMOS) data files. Note that a number of quantities or interaction function parameters in GROMOS are either. Biomolecular Simulation - The GROMOS Software. Reference Manual¶ This part of the documentation covers implementation details of GROMACS. For quick simulation set-up and short explanations, please refer to the User guide. Help with the installation of GROMACS can be found in the Install guide.