Gromacs

Tool Changes for 5.0

    Table of contents
    1. 1. General
    2. 2. g_bond
    3. 3. g_dist
    4. 4. g_sas
    5. 5. g_sgangle
    6. 6. genbox
    7. 7. tpbconv

    (Upcoming) Version 5.0 of GROMACS has changed some of the analysis tools significantly. In the process, some old analysis tools have been removed in favor of more powerful functionality that is available through an alternative tool. This page documents how to perform different tasks that were possible with the old tools with the new set of tools.

    If you've installed an MPI version of the GROMACS tools, then by default the gmx binary is called gmx_mpi and you should adapt accordingly.

    General

    One fundamental change in the organization of the tools is that all tools (and other GROMACS executables as well) are now part of a single gmx binary. They can be run as, e.g., gmx distance <options>, and help can be requested as gmx help distance or gmx distance -h. gmx help produces a list of all available commands. For backwards compatibility, symbolic links are still created by default for old tools: e.g., g_order <options> is equivalent to gmx order <options>, and g_order is simply a symbolic link on the file system.

    New tools mentioned below now accept selections through one or more command-line options instead of prompting for an index group. Please see gmx help selections cmdline for a brief description of how they work in general.

    g_bond

    This tool has been removed in 5.0. A replacement is gmx distance.

    You can provide your existing index file to gmx distance, and it will calculate the same distances. The only difference is that -blen and -tol options have different default values, and that you can control the output histogram with -binw. -aver and -averdist options are not present. Instead, you can choose between the different things to calculate using -oav (corresponds to -d with -averdist), -oall (corresponds to -d without -averdist), -oh (corresponds to -o with -aver), and -oallstat (corresponds to -l without -aver). You can produce any combination of output files. Compared to g_bond, gmx distance -oall is currently missing labels for the output columns.

    g_dist

    This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).

    If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:

    gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall

    The -intra switch is replaced with -nopbc.

    If you used -dist D, you can do the same calculation with gmx select:

    gmx select -n index.ndx -select 'group "B" and within D of com of group "A"' -on/-oi/-os/-olt

    You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt)

    g_sas

    This tool has been rewritten in 5.0, and renamed to gmx sasa.

    The main difference in the new tool is support for selections. Instead of prompting for an index group, a (potentially dynamic) selection for the calculation can be given with -surface. Any number of output groups can be given with -output. The total area of the -surface group is now always calculated. Please see gmx sasa -h.

    The tool no longer automatically divides the surface into hydrophobic and hydrophilic areas, and there is no -f_index option. The same effects can be obtained by defining suitable selections for -output. If you want output that contains the same numbers as with the old tool for a calculation group A and output group B, you can use

    gmx sasa -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B" and not charge {-0.2 to 0.2}; "Total" group "B"'

    Solvation free energy estimates are now calculated only if separately requested with -odg, and are written into a separate file.

    Output option -i for a position restraint file is not currently implemented in the new tool, but would not be very difficult to add if requested.

    g_sgangle

    This tool has been removed in 5.0. A replacement is gmx gangle (for angle calculation) and gmx distance (for -od, -od1, -od2).

    If you had index groups A and B in index.ndx for g_sgangle, you can use the following command to compute the same angle with gmx gangle:

    gmx gangle -n index.ndx -g1 vector/plane -group1 'group "A"' -g2 vector/plane -group2 'group "B"' -oav

    You need to select either vector or plane for the -g1 and -g2 options depending on which one your index groups specify.

    If you only had a single index group A in index.ndx and you used g_sgangle -z or -one, you can use:

    gmx gangle -n index.ndx -g1 vector/plane -group1 'group "A"' -g2 z/t0 -oav

    For the distances, you can use gmx distance to compute one or more distances as you want. Both distances between centers of groups or individual atoms are supported using the new selection syntax.

    genbox

    This tool has been split to gmx solvate and gmx insert-molecules.

    tpbconv

    This tool has been renamed gmx convert-tpr.

    Page last modified 15:08, 18 May 2015 by mabraham