deploy: aaffbee

_sources/user-guide/configs/configs-for-run.rst.txt

@@ -304,7 +304,7 @@ A Simple Configuration Example:  Polymerizing styrene
 
 Consider the following methodological description:
 
-A system of 100 molecules of styrene was prepared by initially placing 100 styrene molecules in a box at a density of 0.3 g/cc.  This system was minimized and subjected to 10 ps of NVT MD at 300 K and then 200 ps of NPT MD at 300 K and 10 bar.  The pressure was reduced to 1 bar and NPT MD was run for an additional 200 ps.  The system was then put through two cycles of constant-pressure annealing at 1 bar in which a cycle is 20 ps at 300 K, 20 ps of linear temperature increase to 600 K, 20 ps at 600 K, and 20 ps of linear temperature decrease back to 300 K.  This is followed by 100 ps of equilibration at 1 bar and 300 K.  The the CURE algorithm was used with an initial search radius of 0.5 nm and increment of 0.25 nm to create new intermonomer bonds until a conversion of 95% was reached.  At each CURE iteration, the system is driven using a series of steered MD simulations to first force all pairs of atoms designated to be bonded but are more than 0.6 nm apart to approach one another to within 0.3 nm. When all such designated pairs are within 0.3 nm of each other, any sacrificial H's are deleted and new bonds and accompanying angles and dihedrals are introduced into the topology.  The bond lengths are then linearly reduced to their equilibrium values through a series of MD simulations.  Once all bonds are at their equilibrium lengths, the iteration is completed by a 100 ps NPT MD simulation at 1 bar and 300 K, before beginning the next CURE iteration.Following CURE, the system was again annealed following the previous protocol and then NPT equilibrated at 1 bar and 300 K for 200 ps.
+A system of 100 molecules of styrene was prepared by initially placing 100 styrene molecules in a box at a density of 0.3 g/cc.  This system was minimized and subjected to 10 ps of NVT MD at 300 K and then 200 ps of NPT MD at 300 K and 10 bar.  The pressure was reduced to 1 bar and NPT MD was run for an additional 200 ps.  The system was then put through two cycles of constant-pressure annealing at 1 bar in which a cycle is 20 ps at 300 K, 20 ps of linear temperature increase to 600 K, 20 ps at 600 K, and 20 ps of linear temperature decrease back to 300 K.  This was followed by 100 ps of equilibration at 1 bar and 300 K.  Then the CURE algorithm was used with an initial search radius of 0.5 nm and increment of 0.25 nm to create new intermonomer bonds until a conversion of 95% was reached.  At each CURE iteration, the system was driven using a series of steered MD simulations to first force all pairs of atoms designated to be bonded but are more than 0.6 nm apart to approach one another to within 0.3 nm. When all such designated pairs were within 0.3 nm of each other, any sacrificial H's were deleted and new bonds and accompanying angles and dihedrals were introduced into the topology.  The bond lengths were then linearly reduced to their equilibrium values through a series of MD simulations.  Once all bonds were at their equilibrium lengths, the iteration was completed by a 100 ps NPT MD simulation at 1 bar and 300 K, before beginning the next CURE iteration.  Following CURE, the system was again annealed following the previous protocol and then NPT equilibrated at 1 bar and 300 K for 200 ps.
 
 A simple YAML ``htpolynet run`` configuration file that encodes this description might look like this.
 

user-guide/configs/configs-for-run.html

@@ -664,7 +664,7 @@
 <section id="a-simple-configuration-example-polymerizing-styrene">
 <span id="configuration-run-example"></span><h2>A Simple Configuration Example:  Polymerizing styrene<a class="headerlink" href="#a-simple-configuration-example-polymerizing-styrene" title="Link to this heading">¶</a></h2>
 <p>Consider the following methodological description:</p>
-<p>A system of 100 molecules of styrene was prepared by initially placing 100 styrene molecules in a box at a density of 0.3 g/cc.  This system was minimized and subjected to 10 ps of NVT MD at 300 K and then 200 ps of NPT MD at 300 K and 10 bar.  The pressure was reduced to 1 bar and NPT MD was run for an additional 200 ps.  The system was then put through two cycles of constant-pressure annealing at 1 bar in which a cycle is 20 ps at 300 K, 20 ps of linear temperature increase to 600 K, 20 ps at 600 K, and 20 ps of linear temperature decrease back to 300 K.  This is followed by 100 ps of equilibration at 1 bar and 300 K.  The the CURE algorithm was used with an initial search radius of 0.5 nm and increment of 0.25 nm to create new intermonomer bonds until a conversion of 95% was reached.  At each CURE iteration, the system is driven using a series of steered MD simulations to first force all pairs of atoms designated to be bonded but are more than 0.6 nm apart to approach one another to within 0.3 nm. When all such designated pairs are within 0.3 nm of each other, any sacrificial H’s are deleted and new bonds and accompanying angles and dihedrals are introduced into the topology.  The bond lengths are then linearly reduced to their equilibrium values through a series of MD simulations.  Once all bonds are at their equilibrium lengths, the iteration is completed by a 100 ps NPT MD simulation at 1 bar and 300 K, before beginning the next CURE iteration.Following CURE, the system was again annealed following the previous protocol and then NPT equilibrated at 1 bar and 300 K for 200 ps.</p>
+<p>A system of 100 molecules of styrene was prepared by initially placing 100 styrene molecules in a box at a density of 0.3 g/cc.  This system was minimized and subjected to 10 ps of NVT MD at 300 K and then 200 ps of NPT MD at 300 K and 10 bar.  The pressure was reduced to 1 bar and NPT MD was run for an additional 200 ps.  The system was then put through two cycles of constant-pressure annealing at 1 bar in which a cycle is 20 ps at 300 K, 20 ps of linear temperature increase to 600 K, 20 ps at 600 K, and 20 ps of linear temperature decrease back to 300 K.  This was followed by 100 ps of equilibration at 1 bar and 300 K.  Then the CURE algorithm was used with an initial search radius of 0.5 nm and increment of 0.25 nm to create new intermonomer bonds until a conversion of 95% was reached.  At each CURE iteration, the system was driven using a series of steered MD simulations to first force all pairs of atoms designated to be bonded but are more than 0.6 nm apart to approach one another to within 0.3 nm. When all such designated pairs were within 0.3 nm of each other, any sacrificial H’s were deleted and new bonds and accompanying angles and dihedrals were introduced into the topology.  The bond lengths were then linearly reduced to their equilibrium values through a series of MD simulations.  Once all bonds were at their equilibrium lengths, the iteration was completed by a 100 ps NPT MD simulation at 1 bar and 300 K, before beginning the next CURE iteration.  Following CURE, the system was again annealed following the previous protocol and then NPT equilibrated at 1 bar and 300 K for 200 ps.</p>
 <p>A simple YAML <code class="docutils literal notranslate"><span class="pre">htpolynet</span> <span class="pre">run</span></code> configuration file that encodes this description might look like this.</p>
 <div class="highlight-YAML notranslate"><div class="highlight"><pre><span></span><span class="nt">Title</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">polystyrene</span>
 <span class="nt">constituents</span><span class="p">:</span>