.. _gmx insert-molecules: gmx insert-molecules ==================== Synopsis -------- .. parsed-literal:: gmx insert-molecules [:strong:`-f` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-ci` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-ip` :emphasis:`[<.dat>]`] [:strong:`-o` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-box` :emphasis:``] [:strong:`-nmol` :emphasis:``] [:strong:`-try` :emphasis:``] [:strong:`-seed` :emphasis:``] [:strong:`-radius` :emphasis:``] [:strong:`-scale` :emphasis:``] [:strong:`-dr` :emphasis:``] [:strong:`-rot` :emphasis:``] Description ----------- ``gmx insert-molecules`` inserts ``-nmol`` copies of the system specified in the ``-ci`` input file. The insertions take place either into vacant space in the solute conformation given with ``-f``, or into an empty box given by ``-box``. Specifying both ``-f`` and ``-box`` behaves like ``-f``, but places a new box around the solute before insertions. Any velocities present are discarded. By default, the insertion positions are random (with initial seed specified by ``-seed``). The program iterates until ``-nmol`` molecules have been inserted in the box. Molecules are not inserted where the distance between any existing atom and any atom of the inserted molecule is less than the sum based on the van der Waals radii of both atoms. A database (``vdwradii.dat``) of van der Waals radii is read by the program, and the resulting radii scaled by ``-scale``. If radii are not found in the database, thoseatoms are assigned the (pre-scaled) distance ``-radius``. A total of ``-nmol`` * ``-try`` insertion attempts are made before giving up. Increase ``-try`` if you have several small holes to fill. Option ``-rot`` specifies whether the insertion molecules are randomly oriented before insertion attempts. Alternatively, the molecules can be inserted only at positions defined in positions.dat (``-ip``). That file should have 3 columns (x,y,z), that give the displacements compared to the input molecule position (``-ci``). Hence, if that file should contain the absolute positions, the molecule must be centered on (0,0,0) before using ``gmx insert-molecules`` (e.g. from :doc:`gmx editconf ` ``-center``). Comments in that file starting with # are ignored. Option ``-dr`` defines the maximally allowed displacements during insertial trials. ``-try`` and ``-rot`` work as in the default mode (see above). Options ------- Options to specify input files: ``-f`` [<.gro/.g96/...>] (protein.gro) (Optional) Existing configuration to insert into: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`tpr` ``-ci`` [<.gro/.g96/...>] (insert.gro) Configuration to insert: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`tpr` ``-ip`` [<.dat>] (positions.dat) (Optional) Predefined insertion trial positions Options to specify output files: ``-o`` [<.gro/.g96/...>] (out.gro) Output configuration after insertion: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp Other options: ``-box`` (0 0 0) Box size (in nm) ``-nmol`` (0) Number of extra molecules to insert ``-try`` (10) Try inserting ``-nmol`` times ``-try`` times ``-seed`` (1997) Random generator seed ``-radius`` (0.105) Default van der Waals distance ``-scale`` (0.57) Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water. ``-dr`` (0 0 0) Allowed displacement in x/y/z from positions in ``-ip`` file ``-rot`` Rotate inserted molecules randomly: xyz, z, none .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at .