started adding ether trappe-ua to forcefield

Author: richardjgowers

foyer/forcefields/trappe-ua.xml

@@ -1,6 +1,7 @@
 <ForceField>
  <AtomTypes>
   <Type name="O" class="O" element="O" mass="15.99940" def="OH" desc="Oxygen in hydroxyl" doi="10.1021/jp003882x"/>
+  <Type name="O_C" class="O_C" element="O" mass="15.99940" def="O([_CH3,_CH2,_HC,C])[_CH3,_CH2,_HC,C]" desc="Oxygen in ether" doi="ethers"/>
   <Type name="H" class="H" element="H" mass="1.00800" def="HO" desc="Hydrogen in hydroxyl" doi="10.1021/jp003882x"/>
   <Type name="CH4" class="CH4" element="_CH4" mass="16.04300" def="_CH4" desc="CH4, united atom" doi="10.1021/jp972543+"/>
   <Type name="CH3_O" class="CH3" element="_CH3" mass="15.03500" def="[_CH3;X1]OH" desc="CH3, united atom, attached to hydroxyl" doi="10.1021/jp003882x"/>
@@ -11,6 +12,7 @@
   <Type name="CH_sp3" class="CH" element="_HC" mass="13.01900" def="[_HC;X3]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])[_CH3,_CH2,_HC,C]" desc="Alkane CH, united atom" doi="10.1021/jp984742e"/>
   <Type name="C_O" class="C" element="C" mass="12.01100" def="[C;X4]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])OH" desc="Carbon attached to hydroxyl" doi="10.1021/jp003882x"/>
   <Type name="C_sp3" class="C" element="C" mass="12.01100" def="[C;X4]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])[_CH3,_CH2,_HC,C]" desc="Alkane carbon" doi="10.1021/jp984742e"/>
+  <Type name="CH3_OC" class="CH3" element="_CH3" mass="12.01100" def="[_CH3;X1]O[_CH3,_CH2,_HC,C]" desc="CH3 in ether" doi="ethers"/>
   <!--
   <Type name="CH2_sp2" class="CH2_E" element="_CH2" mass="14.02700" def="[_CH2;X1][_CH2,_CH,C]" desc="Alkene CH2" doi="10.1021/jp001044x"/>
   <Type name="CH_sp2" class="CH_E" element="_CH" mass="13.01900" def="[_CH;X2](_CH3,_CH2,_CH,C)[_CH2,_CH,C]" desc="Alkene CH" doi="10.1021/jp001044x"/>
@@ -44,6 +46,8 @@
   <Bond class1="CH2" class2="O" length="0.1430" k="502416.0"/>
   <Bond class1="CH" class2="O" length="0.1430" k="502416.0"/>
   <Bond class1="C" class2="O" length="0.1430" k="502416.0"/>
+  <!-- CHX-OC -->
+  <Bond class1="CH3" class2="O_C" length="0.1410" k="502416.0"/>
   <!-- O-H -->
   <Bond class1="O" class2="H" length="0.0945" k="502416.0"/>
   <!-- CHX-CHY alkenes -->
@@ -112,6 +116,17 @@
   <Angle class1="CH2" class2="O" class3="H" angle="1.89368" k="460.62120"/>
   <Angle class1="CH" class2="O" class3="H" angle="1.89368" k="460.62120"/>
   <Angle class1="C" class2="O" class3="H" angle="1.89368" k="460.62120"/>
+  <!-- CHX-[O]-CHY -->
+  <Angle class1="CH3" class2="O_C" class3="CH3" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH3" class2="O_C" class3="CH2" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH3" class2="O_C" class3="CH" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH3" class2="O_C" class3="C" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH2" class2="O_C" class3="CH2" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH2" class2="O_C" class3="CH" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH2" class2="O_C" class3="C" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH" class2="O_C" class3="CH" angle="1.95477" k="502.19338"/>
+  <Angle class1="CH" class2="O_C" class3="C" angle="1.95477" k="502.19338"/>
+  <Angle class1="C" class2="O_C" class3="C" angle="1.95477" k="502.19338"/>
  </HarmonicAngleForce>
  <RBTorsionForce>
   <!-- CHX-[CH2]-[CH2]-CHY -->
@@ -199,9 +214,11 @@
  </RBTorsionForce>
  <NonbondedForce coulomb14scale="0" lj14scale="0">
   <Atom type="O" charge="-0.700" sigma="0.302" epsilon="0.773245"/>
+  <Atom type="O_C" charge="0.0" sigma="1" epsilon="1"/>
   <Atom type="H" charge="0.435" sigma="1.0" epsilon="0.0"/>
   <Atom type="CH4" charge="0.0" sigma="0.373" epsilon="1.23054"/>
   <Atom type="CH3_O" charge="0.265" sigma="0.375" epsilon="0.814817"/>
+  <Atom type="CH3_OC" charge="0.265" sigma="0.375" epsilon="0.814817"/>
   <Atom type="CH3_sp3" charge="0.0" sigma="0.375" epsilon="0.814817"/>
   <Atom type="CH2_O" charge="0.265" sigma="0.395" epsilon="0.382465"/>
   <Atom type="CH2_sp3" charge="0.0" sigma="0.395" epsilon="0.382465"/>

foyer/tests/implemented_trappe_tests.txt

@@ -8,3 +8,4 @@ methane
 methanol
 neopentane
 propane
+dimethylether

foyer/trappe_validation/dimethylether/dme.mol2

@@ -0,0 +1,14 @@
+@<TRIPOS>MOLECULE
+DME
+3 2 1 0 1
+SMALL
+USER_CHARGES
+@<TRIPOS>ATOM
+       1 _CH3        12.5360     1.0140    22.0490 CH3_OC        1 DME        0.265000
+       2 O           13.5570     1.3980    22.8620 O_C           1 DME        0.000000
+       3 _CH3        13.5710     2.7160    23.1980 CH3_OC        1 DME        0.265000
+@<TRIPOS>BOND
+       1        1        2 1
+       2        2        3 1
+@<TRIPOS>SUBSTRUCTURE
+       1 DME             1 RESIDUE    0 1    ROOT      0