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--- exercises:2015_ethz_mmm:md_ala [2015/03/13 08:39] – yakutovich
+++ exercises:2015_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 3: / Line 3: @@
 <note warning>
 TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
-you@eulerX ~$ module load courses mmm vmd ; mmm-init
+you@eulerX ~$ module load courses mmm vmd
+you@eulerX ~$ mmm-init
 </note>
@@ Line 36: / Line 39: @@
 You will start from a configuration already computed in the second lecture (**inp.a.pdb**) which is included in the repository of this exercise as well.
 Update the following part of the file **inp.nve** for the first simulation:
-<note tip>
-To get more information, please visit cp2k reference manual, section Molecular Dynamics:
-http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD.html
-</note>
 <code - md_part.inp.nve>
@@ Line 50: / Line 50: @@
 </code>
+<note tip>
+To get more information, please visit **cp2k reference manual**, section **Molecular Dynamics**:
+http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD.html
+</note>
   * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs. Use 100 K as an initial temperature!
@@ Line 118: / Line 122: @@
 </code>
-Edit the inp.100 file (Put there: NPT ensemble, 100000 steps of simulation, 100 K, Nose-Hoover thermostat and 1.0 fs of timestep). The first simulation is done at 100 K:
+Edit the inp.100 file (Put there: NVT ensemble, 100000 steps of simulation, 100 K, Nose-Hoover thermostat and 1.0 fs of timestep). The first simulation is done at 100 K:
 <code bash>
 you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100