Differences

This shows you the differences between two versions of the page.

--- exercises:2016_ethz_mmm:md_ala [2016/03/16 22:59] – yakutovich
+++ exercises:2016_ethz_mmm:md_ala [2016/03/17 15:00] – yakutovich
@@ Line 1: / Line 1: @@
 ====== Molecular Dynamics simulation of a small molecule======
-<note warning>
-TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
-you@eulerX ~$ module load courses mmm vmd
-you@eulerX ~$ mmm-init
-</note>
@@ Line 101: / Line 94: @@
 Now you will perform a constant Temperature simulations, where the system is in contact with a thermostat, and the conserved quantity includes the thermostat degrees of freedom.
-<note tip>
+<note important>
 Concerning temperature control, in these exercises we will use the NOSE-HOOVER chains method. This has been briefly described in the lecture, and is presented in [[doi>10.1063/1.463940|this paper]] by Glenn Martyna (1992).
 </note>
@@ Line 126: / Line 119: @@
 you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100
 </code>
-  * Then, perform another simulation, using the restart file from the previous simulation: **inp.300**. But first you have to edit it exactly like in the previous case, but **put 300 K** instead of 100 K
+  * Then, perform another simulation, using the restart file from the previous simulation: **inp.300**. But first you have to edit it exactly like in the previous case, except of the temperature which you set as ** 300 K** instead of 100 K
 <code bash>
 you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300