finish tutorial

Author: ajfriedman22

docs/examples/tutorial_2/MTREXEE.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+#SBATCH --nodes 1
+#SBATCH --partition=amilan
+#SBATCH --ntasks=20
+#SBATCH --job-name=tutorial
+#SBATCH --qos=normal
+#SBATCH --time=03:00:00
+#SBATCH --output=tutorial.out
+
+source /projects/anfr8476/pkgs/gromacs-2022.5-wl/bin/GMXRC
+ml gcc
+ml openmpi/5.0.6
+
+conda activate EEXE
+
+mpirun -np 5 run_REXEE -y params.yaml
+
+mpirun -np 5 analyze_REXEE -y params.yaml

docs/examples/tutorial_2/MT_REXEE.ipynb

@@ -0,0 +1,50 @@
+[ moleculetype ]
+; molname       nrexcl
+NA              1
+
+[ atoms ]
+; id    at type         res nr  residu name     at name  cg nr  charge
+1       Na              1       NA              NA       1      1.00000
+
+[ moleculetype ]
+; molname       nrexcl
+CL              1
+
+[ atoms ]
+; id    at type         res nr  residu name     at name  cg nr  charge
+1       Cl              1       CL              CL       1      -1.00000
+
+[ moleculetype ]
+; molname	nrexcl
+SOL		2
+
+[ atoms ]
+; id  at type     res nr  res name  at name  cg nr  charge    mass
+  1   OW          1       SOL       OW       1      -0.834    16.00000
+  2   HW          1       SOL       HW1      1       0.417     1.00800
+  3   HW          1       SOL       HW2      1       0.417     1.00800
+
+#ifndef FLEXIBLE
+
+[ settles ]
+; OW	funct	doh	dhh
+1       1       0.09572 0.15139
+
+[ exclusions ]
+1	2	3
+2	1	3
+3	1	2
+
+#else
+
+[ bonds ]
+; i     j       funct   length  force_constant
+1       2       1       0.09572 502416.0   0.09572        502416.0 
+1       3       1       0.09572 502416.0   0.09572        502416.0 
+        
+
+[ angles ]
+; i     j       k       funct   angle   force_constant
+2       1       3       1       104.52  628.02      104.52  628.02  
+
+#endif