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--- exercise:mm_uzh:nacl_free_energy [2014/05/19 21:45] – talirz
+++ exercise:mm_uzh:nacl_free_energy [2014/06/30 11:25] – talirz
@@ Line 24: / Line 24: @@
 Now, we are ready to move to a more realistic system -- NaCl in water.
-We have performed constrained MD of NaCl in water and saved the trajectory of the corresponding Lagrange multipliers.
+We have performed constrained MD of NaCl in water and saved the trajectory of the corresponding Lagrange multipliers (ask your teaching assistant).
 The script ''./integrate.sh'' computes the average values of the Shake Lagrange multipliers and uses them to perform the free energy integration.
@@ Line 41: / Line 41: @@
-We have provided a trajectory spanning 50 ns of unconstrained molecular dynamics of NaCl in water. The individual frames are spaced by 1 ps in order to reduce correlation between subsequent frames.
+We have performed a trajectory spanning 50 ns of unconstrained molecular dynamics of NaCl in water (ask your teaching assistant). The individual frames are spaced by 1 ps in order to reduce correlation between subsequent frames.
 <note>**TASK 4**
-  - In the [[http://cp2k.org/exercise:mm_uzh:h2o_md|previous exercise]], we computed the O-O radial distribution function for water with reasonable statistics using just 20 ps of simulated time. Give at least one reason, why collecting enough statistics for the Na-Cl radial distribution function requires much longer simulation times (with our setup).
+  - In the [[http://cp2k.org/exercise:mm_uzh:h2o_md|previous exercise]], we computed the O-O radial distribution function for water with acceptable statistics using just 20 ps of simulated time. Give two reasons, why collecting enough statistics for the Na-Cl radial distribution function requires much longer simulation times (with our setup).
   - Compute the radial distribution function for the provided trajectory and plot it as a function of Na-Cl distance.
   - Use the equations above to compute the free energy profile. Does it agree with the one constructed from the Shake Lagrange multipliers?
 </note>