Advanced topics
===============

Used external packages
----------------------

GROMACS
~~~~~~~

`Link to Homepage <https://manual.gromacs.org/documentation/>`

DL\_POLY
~~~~~~~~

`Link to Homepage <https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx>`


DL\_POLY interface
------------------

**WARNING: The DL\_POLY interface is still experimental (in development)
. The Force Matching might work as well, although it has
not been tested thoroughly.**


The DL\_POLY interface fully supports coarse-grain mapping of a full-atom
system previuosly simulated with any version of DL\_POLY, including
DL\_POLY-Classic. However, the full optimization of the effective
potentials with the aid of iterative methods will only become possible
when the new release of DL\_POLY-4 (4.06) is made public; the reason
being the incapability of earlier DL\_POLY versions of using
user-specified tabulated force-fields for intramolecular, aka “bonded”,
interactions: bonds, angles, dihedral angles (torsions). Below the
coarse-graining and CG force-field optimization with the aid of the
latest DL\_POLY-4 version (4.06+) are outlined.

Running VOTCA with DL\_POLY-4 as MD simulation engine is very similar to
doing so with GROMACS. The three types of required input files in the
case of DL\_POLY are: CONTROL – containing the simulation directives and
parameters (instead of ``.mdp`` file for GROMACS), FIELD – the topology
and force-field specifications (instead of ``.top`` and ``.tpr`` files),
and CONFIG (instead of ``.gro`` file) – the initial configuration file,
containing the MD cell matrix and particle coordinates (it can also
include initial velocities and/or forces); for details see
DL\_POLY-4 manual. Most of the VOTCA tools and scripts described above in
the case of using GROMACS will work in the same manner, with the
following conventional substitutions for the (default) file names used
in options for VOTCA scripts, as necessary:

.. code:: none

    .dlpf = the topology read from FIELD or written to FIELD_CGV
    .dlpc = the configuration read from CONFIG or written to CONFIG_CGV
    .dlph = the trajectory read from HISTORY or written to HISTORY_CGV

It is also possible to specify file names different from the standard
DL\_POLY convention, in which case the user has to use the corresponding
dot-preceded extension(s); for example: FA-FIELD.dlpf instead of FIELD
or CG-HISTORY.dlph instead of HISTORY\_CGV (see
:ref:`reference_programs`, as well as the man pages or output of
VOTCA commands, with option ``--help``).

VOTCA follows the DL\_POLY conventions for file names and formats. Thus,
``csg_dlptopol`` and ``csg_map`` produce the CG topology (FIELD\_CGV by
default), configuration (CONFIG\_CGV), and/or trajectory (HISTORY\_CGV)
files fully compatible with and usable by DL\_POLY. **Note that the
ability of these tools to read and write a plethora of different file
formats provides means to convert input and output files between the
simulation packages supported by VOTCA, e.g. GROMACS – DL\_POLY or vice
versa. The user is, however, strongly advised to check the resulting
files for consistency before using them).**

Similarly, the distribution analysis and potential/force generation
utilities, such as ``csg_stat`` and VOTCA scripts, will read and write
DL\_POLY-formatted files; in particular, the tabulated force-field files
containing the potential and force/virial data: TABLE – for short-range
(VdW) “non-bonded” interactions, TABBND, TABANG and TABDIH – for
“bonded” interations: bonds, bending angles and dihedrals,
correspondingly (for the format details see DL\_POLY-4 manual). Note,
however, that the latter three files can only be used by
DL\_POLY-4 (4.06+).

The user is advised to search for “dlpoly” through the
``csg_defaults.xml``, ``csg_table`` files and in scripts located in
``share/votca/scripts/inverse/`` in order to find out about the xml-tags
and options specific for DL\_POLY; see also :ref:`reference_settings_file`
and :ref:`reference_scripts`.
