Merge branch 'master' of github.com:mlund/faunus

Author: mlund

README.md

@@ -1,7 +1,6 @@
 [![Documentation](https://readthedocs.org/projects/faunus/badge/?version=latest)](https://faunus.readthedocs.io/en/latest/?badge=latest)
 [![Build Status](https://app.travis-ci.com/mlund/faunus.svg?branch=master)](https://app.travis-ci.com/mlund/faunus)
 [![License: MIT](https://img.shields.io/badge/License-MIT-brightgreen.svg)](https://opensource.org/licenses/MIT)
-[![Anaconda-Server Badge](https://anaconda.org/conda-forge/faunus/badges/installer/conda.svg)](https://anaconda.org/conda-forge/faunus)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/2ac7217d373a4f34a2dae2d912c9d1a1)](https://www.codacy.com/app/mlund/faunus?utm_source=github.com&utm_medium=referral&utm_content=mlund/faunus&utm_campaign=Badge_Grade)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5235137.svg)](https://doi.org/10.5281/zenodo.5235137)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/faunus/badges/platforms.svg)](https://anaconda.org/conda-forge/faunus)

docs/_docs/topology.md

@@ -260,9 +260,11 @@ The following keywords for each molecule type are available:
 `translate=[0,0,0]`  | Displace loaded `positions` with vector
 
 A filename with positions for the `N` molecules can be given with `positions`.
-The file must contain exactly `N`-times molecular
+The trajectory-like file must contain exactly `N` frames with molecular
 positions that must all fit within the simulation box. Only _positions_ from
 the file are copied; all other information is ignored.
+When using `positions`, `keepos` should be set to true. See also
+[this issue](https://github.com/mlund/faunus/issues/268#issuecomment-618904639) on github.
 
 For `implicit` molecules, only `N` should be given and the molecules are never
 inserted into the simulation box.

examples/fasta-titration.yml renamed to examples/fasta/fasta.yml

@@ -1,4 +1,9 @@
 #!/usr/bin/env yason.py
+#
+# A peptide chain is generated from a FASTA sequence and
+# then titrated using a constant pH / constant salt ensemble
+# with explicit salt particles and counter-ions.
+# 
 {% set eps = 0.05 %}
 {% set pH = 7.0 %}
 {% set Cs = 0.010 %}