###############################################
 Conformational Sampling & Dynamics (Gaussian)
###############################################

This page covers CREST conformational searches and trajectory analysis using Gaussian.

************
 CREST Jobs
************

CREST (Conformer-Rotamer Ensemble Sampling Tool) performs systematic conformational searches to find low-energy
conformers. CHEMSMART combines CREST with Gaussian for subsequent calculations.

.. code:: bash

   chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] crest -j <jobtype> [SUBCMD_OPTIONS]

CREST Options
=============

.. list-table::
   :header-rows: 1
   :widths: 30 15 55

   -  -  Option
      -  Type
      -  Description

   -  -  ``-j, --jobtype``
      -  string
      -  Job type: opt, ts, modred, scan, sp (required)

   -  -  ``-nc, --num-confs-to-run``
      -  int
      -  Number of conformers to process

.. warning::

   The ``-j, --jobtype`` option is required for CREST jobs.

Basic Usage
===========

Run optimization on CREST conformers:

.. code:: bash

   chemsmart sub gaussian -p project -f crest_conformers.xyz -c 1 -m 1 crest -j opt

Run TS optimization on conformers:

.. code:: bash

   chemsmart sub gaussian -p project -f crest_conformers.xyz -c 0 -m 1 crest -j ts

Run modred optimization with constraints:

.. code:: bash

   chemsmart sub gaussian -p project -f crest_conformers.xyz -c 0 -m 2 crest -j modred -c [1,4]

.. note::

   The ``<input_file>`` is typically the CREST output file named ``crest_conformers.xyz``.

Examples
========

Process 10 lowest-energy conformers:

.. code:: bash

   chemsmart sub gaussian -p project -f crest_conformers.xyz -l structure_from_lowest -c 0 -m 1 crest -j opt -nc 10

Output files are named ``structure_from_lowest_opt_c1`` through ``structure_from_lowest_opt_c10``.

.. note::

   If a job terminates before all conformers are processed (e.g., walltime limit), resubmitting will continue from where
   it left off.

*********************
 Trajectory Analysis
*********************

Process molecular dynamics trajectories and extract structures for further analysis:

.. code:: bash

   chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] traj -j <jobtype> [SUBCMD_OPTIONS]

Trajectory Options
==================

.. list-table::
   :header-rows: 1
   :widths: 30 15 55

   -  -  Option
      -  Type
      -  Description

   -  -  ``-j, --jobtype``
      -  string
      -  Job type: opt, ts, modred, scan, sp (required)

   -  -  ``-ns, --num-structures-to-run``
      -  int
      -  Number of structures from the end of trajectory to process

   -  -  ``-x, --proportion-structures-to-use``
      -  float
      -  Proportion of trajectory to use (0.0 < x <= 1.0, default: 0.1) At least one structure is always selected.

.. warning::

   The ``-j, --jobtype`` option is required for trajectory analysis.

Basic Usage
===========

Process trajectory structures:

.. code:: bash

   chemsmart sub gaussian -p project -f trajectory.xyz -c 0 -m 1 traj -j opt

Use the last 30% of trajectory:

.. code:: bash

   chemsmart sub gaussian -p project -f md.traj -c 0 -m 1 traj -j opt -x 0.3

*******************************************
 Grouper Options for CREST/Trajectory Jobs
*******************************************

Please check

-  :doc:`grouper-crest-or-traj-workflow`

for more details about this workflow.