update README mdp options to RAMD-2

README.md

@@ -10,51 +10,59 @@ applied to a molecule in the system.
 
 ## Installation
 
-See http://manual.gromacs.org/documentation/2019/install-guide/index.html
+See http://manual.gromacs.org/documentation/2020/install-guide/index.html
 
 ## HPC deployment with EasyBuild
 
-The [EasyBuild](http://easybuilders.github.io/easybuild/) recipe is available [here](https://github.com/BerndDoser/easybuild-easyconfigs/blob/hits/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-RAMD-1.0-fosscuda-2019b.eb). 
+The [EasyBuild](http://easybuilders.github.io/easybuild/) recipe is available [here](https://github.com/BerndDoser/easybuild-easyconfigs/blob/hits/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.5-RAMD-2.0-fosscuda-2019b.eb). 
 
 ## Usage
 
 Please use following mdp options:
 
- * ramd: Switch on RAMD
- * ramd-receptor
- * ramd-ligand
- * ramd-force: The force constant
+ * ramd
 
-   For a set of compounds with the dissociation rate expected to vary
-   within the range of 0.1-0.0001 1/s, a random force magnitude of 600
-   kJ/mol/nm can be applied. If necessary, the force magnitude can be
-   adjusted according to the longest and shortest dissociation time
-   observed in simulations. The upper threshold of the force magnitude is
-   determined by the fast-dissociated compounds, whose dissociation time
-   should be longer than 100 ps. The lower threshold of the force magnitude
-   depends on the computation facilities available.
+   RAMD will be applied.
 
  * ramd-seed
 
-   Seed for random direction
+   Seed for random direction generator
 
  * ramd-eval-freq
 
    This parameter affect absolute dissociation time but have less
    effect on the relative dissociation times of different compounds. It is
    recommended to use default value.
 
- * ramd-r-min-dist
+ * ramd-force-out-freq
+
+   This ramd parameter resets pull-nstxout and pull-nstfout.
+
+ * ramd-ngroups
+
+   The number of ramd groups defining the ligand-receptor pair.
+   Below only the pull options for group 1 are given,
+   further groups simply increase the group index number.
+
+ * ramd-group1-force
+
+   The force constant in kJ/mol/nm. Default value is 600 kJ/mol/nm.
+   For a set of compounds with the dissociation rate expected to vary
+   within the range of 0.1-0.0001 1/s, a random force magnitude of 600
+   kJ/mol/nm can be applied. If necessary, the force magnitude can be
+   adjusted according to the longest and shortest dissociation time
+   observed in simulations. The upper threshold of the force magnitude is
+   determined by the fast-dissociated compounds, whose dissociation time
+   should be longer than 100 ps. The lower threshold of the force magnitude
+   depends on the computation facilities available.
+
+ * ramd-group1-r-min-dist
 
    This parameter affect absolute dissociation time but have less
    effect on the relative dissociation times of different compounds. It is
    recommended to use default value.
 
- * ramd-force-out-freq
-
-   This ramd parameter resets pull-nstxout and pull-nstfout.
-
- * ramd-max-dist
+ * ramd-group1-max-dist
 
    This value has to be adjusted for the system studied: no
    protein-ligand contacts should be observed in the last snapshot of a
@@ -66,3 +74,25 @@ Please use following mdp options:
    ligand does not interact with the protein, usually has a negligible contribution
    to the observed dissociation time).
 
+ * ramd-group1-receptor
+
+   Receptor for the first RAMD group. Default name is 'Protein'.
+
+ * ramd-group1-ligand
+
+   Ligand for the first RAMD group. Default name is 'INH'.
+
+ * ramd-group1-receptor-pbcatom
+
+   The value will be forwarded to the associated pull group of the receptor.
+   Default value is 0, which takes the middle atom (number wise).
+
+ * ramd-group1-ligand-pbcatom
+
+   The value will be forwarded to the associated pull group of the ligand.
+   Default value is 0, which takes the middle atom (number wise).
+
+ * ramd-pbc-ref-prev-step-com
+
+   The value will be forwarded to pull-pbc-ref-prev-step-com. Default value is 'yes'.
+