Galaxy |

Create GROMACS position restraints files (version 2022+galaxy0)

GRO input file:

Input structure

Index (NDX) file:

Index file containing the atoms which should be restrained

Force constants:

Vector (in Cartesian space) specifying force constants for the restraints (kJ/mol nm^2)

Index of group:

Index of group for calculating position restraints - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).

Generate detailed log:

Generate detailed log information that can be summarized with ParseLog.

What it does

This tool calculates a position restraint (ITP) file for part of a system, specified in provided GRO and NDX files.

Input

GRO structure file.

Index (NDX) file.

Force constant vector (in Cartesian space) for applying restraints. E.g. '1000 1000 1000' will apply a force constraint of 1000 kJ/mol nm^2 along each (XYZ) axis.

Index number of the group for which restraints should be calculated, i.e. the position of the group in the index file.

Output

Position restraint (itp) file, which may be useful for system equilibration.