Changes between Initial Version and Version 1 of TremoloWaterExample

Timestamp:

Apr 6, 2011, 8:10:35 PM (14 years ago)

Author:

FrederikHeber

Comment:

first version

TremoloWaterExample

@@ +1 @@
+== An example with water and TREMOLO ==
+
+We want to create a box filled with water.
+
+First, we need the following file '''singleh2o.data''':
+{{{
+# ATOMDATA Id name resName resSeq x=3 charge type neighbors=2
+# INPUTCONV shift 6.25 6.25 6.25
+# INPUTCONV periodic 1
+# INPUTCONV temp 0.55
+# OUTPUTCONV shift -6.25 -6.25 -6.25
+  1  OH2 TIP3  1   1.583   1.785   1.480 -0.8340  OT    2   3
+  2  H1  TIP3  1   1.186   1.643   2.213  0.4170  HT    1   0
+  3  H2  TIP3  1   2.642   1.896   1.730  0.4170  HT    1   0
+}}}
+
+Take the remainder of the required files (for a TREMOLO simulation) from the respective ''h2o'' example of TREMOLO.
+
+Next, we create a 10x10x10 box filled with water at 1g/cm^3^ by calling molecuilder as follows:
+{{{
+molecuilder --parse-tremolo-potentials h2o.potentials -i h2o.data -o tremolo xyz --change-box "10,0,10,0,0,10" --fill-void singleh2o.data --distances "3.1,3.1,3.1"
+}}}
+
+We explain briefly the function of each action:
+ * ''--parse-tremolo-potentials'': parses a TREMOLO's potentials file. Without it, molecuilder does not know that '''OT''' actually refers to an oxygen atom (with element symbol '''O''')
+ * ''-i'': This is the specification of the output file (also the input file, if it contains atoms already, water is filled around it).
+ * ''--change-box'': We set the box dimension by giving a vector of each edge's lengths.
+ * ''--fill-void'': The empty space in the box (i.e. all of it) is filled with the atoms given by '''singleh2o.data'''. ''--distances'' refers to the distance between each molecule's center per axis (x,y,z). Note that you may also specify ''--random-atom-displacement'', ''--random-molecule-displacement'', and ''--!DoRotate'' to give the maximum random displacement for each atom, each molecule or a general rotation. Note even more that you can specify the random number generator used by the action ''--set-random-number-distribution''. Thereby, you can even have the random angles for rotation drawn from a discrete set and hence generate a discrete set of orientations of the water molecules.
+
+If you are interested in how the last note works, try this:
+{{{
+molecuilder --parse-tremolo-potentials h2o.potentials -i h2o.data -o tremolo xyz --change-box "10,0,10,0,0,10" --set-random-number-distribution uniform_int --random-number-distribution-parameters "min=0;max=4" --fill-void singleh2o.data --distances "3.1,3.1,3.1" --distance-to-boundary 2 --DoRotate 1
+}}}
+
+Now, we need some more parameters:
+ * ''--set-random-number-distribution'': set the random number distribution, here a uniform integral distribution.
+ * ''--random-number-distribution-parameters'': We set min to 0 and max to 4, i.e. we have a five-sided dice.
+ * ''--distance-to-boundary'': Minimum distance to boundary should be 2 for the molecule to be placed, otherwise it is removed.
+ * ''--!DoRotate'': Enable random rotations.