Merge pull request #458 from leeping/master

Added TIP3P-FB and TIP4P-FB water models

docs/usersguide/application.rst

@@ -677,7 +677,9 @@ files:
 File         Water Model                                 
 ===========  ============================================
 tip3p.xml    TIP3P water model\ :cite:`Jorgensen1983`  
+tip3pfb.xml  TIP3P-FB water model\ :cite:`Wang2014`    
 tip4pew.xml  TIP4P-Ew water model\ :cite:`Horn2004`    
+tip4pfb.xml  TIP4P-FB water model\ :cite:`Wang2014`    
 tip5p.xml    TIP5P water model\ :cite:`Mahoney2000`    
 spce.xml     SPC/E water model\ :cite:`Berendsen1987`  
 swm4ndp.xml  SWM4-NDP water model\ :cite:`Lamoureux2006`
@@ -1300,8 +1302,9 @@ water models:
 
     modeller.addSolvent(forcefield, model='tip5p')
 
-Allowed values for the :code:`model` option are 'tip3p', 'spce', 'tip4pew',
-and 'tip5p'.  Be sure to include the single quotes around the value.
+Allowed values for the :code:`model` option are 'tip3p', 'tip3pfb', 'spce', 
+'tip4pew', 'tip4pfb', and 'tip5p'.  Be sure to include the single quotes 
+around the value.
 
 Another option is to add extra ion pairs to give a desired total ionic strength.
 For example:

docs/usersguide/references.bib

@@ -409,3 +409,12 @@
    type = {Journal Article}
 }
 
+@article{Wang2014
+   author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
+   title = {Building force fields: an automatic, systematic, and reproducible approach},
+   journal = {Journal of Physical Chemistry Letters},
+   volume = {5},
+   pages = {1885-1891},
+   year = {2014},
+   type = {Journal Article}
+}

wrappers/python/simtk/openmm/app/data/tip3pfb.xml

+<ForceField>
+ <Info>
+  <DateGenerated>2014-05-28</DateGenerated>
+  <Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. Building force fields - an automatic, systematic and reproducible approach.  Journal of Physical Chemistry Letters, 2014, 5, pp 1885-1891.  DOI:10.1021/jz500737m</Reference>
+ </Info>
+ <AtomTypes>
+  <Type name="tip3p-fb-O" class="OW" element="O" mass="15.99943"/>
+  <Type name="tip3p-fb-H" class="HW" element="H" mass="1.007947"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="tip3p-fb-O"/>
+   <Atom name="H1" type="tip3p-fb-H"/>
+   <Atom name="H2" type="tip3p-fb-H"/>
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <HarmonicBondForce>
+  <Bond class1="OW" class2="HW" length="0.101181082494" k="462750.4"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle class1="HW" class2="OW" class3="HW" angle="1.88754640288" k="836.8"/>
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="tip3p-fb-O" charge="-0.848448690103" sigma="0.317796456355" epsilon="0.652143528104" />
+  <Atom type="tip3p-fb-H" charge="0.4242243450515" sigma="1" epsilon="0" />
+ </NonbondedForce>
+</ForceField>
+

wrappers/python/simtk/openmm/app/data/tip4pfb.xml

+<ForceField>
+ <Info>
+  <DateGenerated>2014-05-28</DateGenerated>
+  <Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. Building force fields - an automatic, systematic and reproducible approach.  Journal of Physical Chemistry Letters, 2014, 5, pp 1885-1891.  DOI:10.1021/jz500737m</Reference>
+ </Info>
+ <AtomTypes>
+  <Type name="tip4p-fb-O" class="OW" element="O" mass="15.99943"/>
+  <Type name="tip4p-fb-H" class="HW" element="H" mass="1.007947"/>
+  <Type name="tip4p-fb-M" class="MW" mass="0"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="tip4p-fb-O"/>
+   <Atom name="H1" type="tip4p-fb-H"/>
+   <Atom name="H2" type="tip4p-fb-H"/>
+   <Atom name="M" type="tip4p-fb-M"/>
+   <VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="8.203146574531e-01" weight2="8.984267127345e-02" weight3="8.984267127345e-02" />
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <HarmonicBondForce>
+  <Bond class1="OW" class2="HW" length="0.09572" k="462750.4"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle class1="HW" class2="OW" class3="HW" angle="1.82421813418" k="836.8"/>
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="tip4p-fb-O" charge="0" sigma="3.165552430462e-01" epsilon="7.492790213533e-01" />
+  <Atom type="tip4p-fb-H" charge="5.258681106763e-01" sigma="1" epsilon="0" />
+  <Atom type="tip4p-fb-M" charge="-1.0517362213526e+00" sigma="1" epsilon="0" />
+ </NonbondedForce>
+</ForceField>