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--- exercise:nacl_md [2014/05/28 12:24] – exercise:free_energy renamed to exercise:nacl_md oschuett
+++ exercise:nacl_md [2014/05/30 12:19] – [Observer NaCl dissociation] oschuett
@@ Line 1: / Line 1: @@
-===== 1. Task: Observer NaCl dissociation =====
+====== Observer NaCl dissociation ======
 Perform a MD simulation of NaCl in water by running the input-file ''NaCl_in_water.inp''.
@@ Line 14: / Line 15: @@
   - Click ''Save'' to store the distance-trajectory
-Plot the obtained distance-trajectory. Does the dissociation occur?
+Plot the obtained distance-trajectory. Does the dissociation occur? If it occurs, does the actual transition happens quickly ? Is dissociation a likely or rare event ? Do you expect an activation energy ?
+<note tip>
+ You should run this calculation on 4 cores with ''bsub -n 4''.
+</note>
 ====== Required Files ======
 <code - NaCl_in_water.inp>
 &GLOBAL
-  PROJECT run-NACL-FREE-MYSEED
+  PROJECT NaCl-Free
   RUN_TYPE MD
 &END GLOBAL
@@ Line 371: / Line 375: @@
 Cl    1.3489457703231567E+01    1.0346547591020910E+01    1.2149103773398551E+01 CLM
      &END COORD
+     &COLVAR
+       &DISTANCE
+         ATOMS 190 191
+       &END DISTANCE
+       &PRINT
+       &END
+    &END COLVAR
     &TOPOLOGY
       CONNECTIVITY GENERATE