/bartender

Primary LanguageGoGNU General Public License v2.0GPL-2.0

Bartender has moved

This repo is only here for compatibility reasons. It is not up to date.

Check out the new repo!

This is Bartender, beta.

Install

To install the binary distribution, uncompress the tgz file to some suitable directory, set the variable BTROOT to that directory, and put the bartender excecutable in the PATH.

To use Bartender, you will also need the xtb program from the Grimme group.

Bartender use

Assuming the Bartender and xtb excecutables are in the PATH, you can use Bartender by:

bartender [flags] Geometry.xyz BartenderInput.inp

The geometry file can also be in PDB or GRO format. The Bartender input format is a simple way of specifying the bonded parameters to be obtained. You can find a sample in the directory of the distribution, under samples/.

The optional flags control the way Bartender behaves. Sensible defaults have been prepared so, in most cases, no flags are needed. Use

bartender -help

To get all the flags available and their use. We document here some of the most common flags:

  • -charge int the total charge of the system, in a.u. (default 0)
  • -method string The method employed in the semiempirical simulation. Valid options are gfn0, gfn1,gfn2 and gfnff (default "gfnff")
  • -time int The total simulation time for the QM MD, in ps. If a number <0 is given, the MD will not be performed, and a previous trajectory will be used (default 1000).
  • -verbose int Sets the level of verbosity
  • -dcdSave filename.dcd Saves the trajectory produced by xtb in the more compact DCD format
  • -owntraj filename Reads a trajectory (DCD, XTC, multiPDB or multiXYZ, identified from the file extension) instead of performing an xtb simulation.

Latest changes:

  1. A REMD can be requested by placing a star (*) near any dihedral in the Bartender input file.
  2. New flags to control the REMD
  3. Instead of "verbose" or "non-verbose" there are now 4 levels of verbosity, from 0 to 3. The default is 1 (on the quiet side)
  4. The default method is now gfnff (it could still change)

REMD

The REMD works by calling another program, the Replica Exchange Engine (REE) which will is open source and on Github, but is also distributed together with bartender as a binary (in the sub-directory RE). You can try the binary on its own (without Bartender) to run REMDs on a given geometry (xtb is requited). It is used as:

./ree OPTIONS geometry.xyz SIMULATION_TIME

Use:

./ree -help

To see the avaliable options