Differences

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--- exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:32] – [Task 2: Perform constrained MD simulations] vrybkin
+++ exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:40] – [Task 3: Evaluate the free energy difference] vrybkin
@@ Line 38: / Line 38: @@
   * To avoid confusion, try to perfrom every task in a new directory
   * You may increase or decrease the number of MD steps, which is set to 5000 in the file, to speed-up the calculation or else get a better statiscics.
-</note>
-⇒ Each constrained MD will produce a ''.LagrangeMultLog''-files, which look like this:
-<code>
-Shake  Lagrangian Multipliers:            -0.054769270
-Rattle Lagrangian Multipliers:            -0.020937479
-Shake  Lagrangian Multipliers:            -0.020937479
-Rattle Lagrangian Multipliers:            -0.020937479
-...
-</code>
-  * From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this:
-<code>
-grep Shake yourprojectname.LagrangeMultLog | awk '{c++ ; s=s+$4}END{print s/c}'
-</code>
-  * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$.
-  * From these forces the free energy difference can be obtained via TI (see **Background**)
-<note warning>
-Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/bohr), while the distances are in Angstrom.
 </note>
@@ Line 74: / Line 53: @@
  &END CONSTRAINT
 </code>
+===== Task 3: Evaluate the free energy difference =====
+⇒ Each constrained MD will produce a ''.LagrangeMultLog''-files, which look like this:
+<code>
+Shake  Lagrangian Multipliers:           -63.547262596
+Rattle Lagrangian Multipliers:            63.240598387
+Shake  Lagrangian Multipliers:            -0.326901815
+Rattle Lagrangian Multipliers:            -0.318145579
+</code>
+<note warning>
+Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/bohr), while the distances are in Angstrom.
+</note>
+  * From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this:
+<code>
+grep Shake yourprojectname.LagrangeMultLog | awk '{c++ ; s=s+$4}END{print s/c}'
+</code>
+  * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$.
+  * From these forces the free energy difference can be obtained via TI (see **Background**)