tried exercice

Author: simongravelle

level1/bulk-solution/exercises/cage-effect/inputs/production.mdp

@@ -1,6 +1,6 @@
 integrator = md
 nsteps = 10000
-dt = 0.001
+dt = 0.0001
 
 comm_mode = linear
 comm_grps = system
@@ -9,9 +9,9 @@ cutoff-scheme = Verlet
 nstlist = 10
 ns_type = grid
 
-nstlog = 5
-nstenergy = 5
-nstxout-compressed = 2
+nstlog = 10
+nstenergy = 10
+nstxout-compressed = 10
 
 vdw-type = Cut-off
 rvdw = 1.0

level1/bulk-solution/exercises/cage-effect/localRun.sh

@@ -1,11 +1,12 @@
 #!/bin/sh
 
-#gmx=/home/simon/Softwares/gromacs-2024.2/build/bin/gmx
-gmx=gmx
+gmx=/home/simon/Softwares/gromacs-2024.2/build/bin/gmx
 
 ${gmx} grompp -f inputs/production.mdp -c npt.gro -p topol.top -o production -pp production -po production
 ${gmx} mdrun -v -deffnm production -nt 8
 
+${gmx} convert-trj -f production.xtc -s production.tpr -o production.xtc -dt 1
+
 ${gmx} msd -f production.xtc -s production.tpr -o na-msd.xvg << EOF
     3
 EOF 

level1/bulk-solution/exercises/cage-effect/na-msd.xvg

@@ -0,0 +1,35 @@
+# This file was created Fri Jun  7 10:10:58 2024
+# Created by:
+#                       :-) GROMACS - gmx msd, 2024.2 (-:
+# 
+# Executable:   /home/simon/Softwares/gromacs-2024.2/build/bin/gmx
+# Data prefix:  /home/simon/Softwares/gromacs-2024.2 (source tree)
+# Working dir:  /home/simon/Git/GROMACS/inputs/level1/bulk-solution/exercises/cage-effect
+# Command line:
+#   gmx msd -f production2.xtc -s production.tpr -o na-msd.xvg
+# gmx msd is part of G R O M A C S:
+#
+# GROtesk MACabre and Sinister
+#
+@    title "Mean Squared Displacement"
+@    xaxis  label "tau (ps)"
+@    yaxis  label "MSD (nm\\S2\\N)"
+@TYPE xy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ s0 legend "D[        Na] = 1.7570 (+/- 0.4286) (1e-5 cm^2/s)"
+      0.000          0
+      1.000  0.0116462
+      2.000  0.0253965
+      3.000  0.0360835
+      4.000  0.0408977
+      5.000  0.0484014
+      6.000  0.0678799
+      7.000  0.0772106
+      8.000   0.086677
+      9.000  0.0965086
+     10.000  0.0912831