more work on trappe-ethers

Author: richardjgowers

foyer/forcefields/trappe-ua.xml

@@ -12,18 +12,18 @@
   <Type name="C_O" class="CHx" 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="CHx" 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_eth" class="CHx" element="_CH3" mass="15.03500" def="[_CH3;X1]O[_CH3,_CH2,_HC,C]" desc="CH3 attached to ether oxygen" doi="ethers"/>
-  <Type name="CH3_Cald" class="CHx" element="_CH3" mass="15.03500" def="[_CH3;X1][_HC]=O" desc="CH3 adjacent to aldehyde C" doi="ethers"/>
+  <Type name="CH3_Cald" class="CHx" element="_CH3" mass="15.03500" def="[_CH3;X1][_HC;X2]O" desc="CH3 adjacent to aldehyde C" doi="ethers"/>
   <Type name="CH2_eth" class="CHx" element="_CH2" mass="14.02700" def="[_CH2;X2]([_CH3,_CH2,_HC,C])O[_CH3,_CH2,_HC,C]" desc="CH2 attached to ether oxygen" doi="ethers"/>
-  <Type name="CH2_Cald" class="CHx" element="_CH2" mass="14.02700" def="[_CH2;X2]([_CH3,_CH2,_HC,C])[_HC]=O" desc="CH2 attached to aldehyde carbon" doi="ethers"/>
+  <Type name="CH2_Cald" class="CHx" element="_CH2" mass="14.02700" def="[_CH2;X2]([_CH3,_CH2,_HC,C])[_HC;X2]O" desc="CH2 attached to aldehyde carbon" doi="ethers"/>
   <Type name="CH_eth" class="CHx" element="_HC" mass="13.01900" def="[_HC;X3]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])O[_CH3,_CH2,_HC,C]" desc="CH, united atom, attached to ether oxygen" doi="ethers"/>
-  <Type name="CH_Cald" class="CHx" element="_HC" mass="13.01900" def="[_HC;X3]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])[_HC]=O" desc="CH, united atom, attached to aldehyde carbon" doi="ethers"/>
+  <Type name="CH_Cald" class="CHx" element="_HC" mass="13.01900" def="[_HC;X3]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])[_HC;X2]O" desc="CH, united atom, attached to aldehyde carbon" doi="ethers"/>
   <Type name="C_eth" class="CHx" element="C" mass="12.01100" def="[C;X4]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])O[_CH3,_CH2,_HC,C]" desc="Carbon attached to ether oxygen" doi="ethers"/>
-  <Type name="C_Cald" class="CHx" element="C" mass="12.01100" def="[C;X4]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])[_HC]=O" desc="Carbon attached to aldehyde carbon" doi="ethers"/>
-  <Type name="CH_ald" class="CHx" element="_HC" mass="13.01900" def="[_HC;X2]([_CH3,_CH2,_HC,C])=O" desc="C in aldehyde" doi="ethers"/>
-  <Type name="C_ket" class="CHx" element="_HC" mass="13.01900" def="[C;X3]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])=O" desc="C in ketone" doi="ethers"/>
+  <Type name="C_Cald" class="CHx" element="C" mass="12.01100" def="[C;X4]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])[_HC;X2]O" desc="Carbon attached to aldehyde carbon" doi="ethers"/>
+  <Type name="CH_ald" class="CHx" element="_HC" mass="13.01900" def="[_HC;X2]([_CH3,_CH2,_HC,C])O" desc="C in aldehyde" doi="ethers"/>
+  <Type name="C_ket" class="CHx" element="_HC" mass="13.01900" def="[C;X3]([_CH3,_CH2,_HC,C])([_CH3,_CH2,_HC,C])O" desc="C in ketone" doi="ethers"/>
   <Type name="O_eth" class="O" element="O" mass="15.99940" def="O([_CH3,_CH2,_HC,C])[_CH3,_CH2,_HC,C]" desc="Oxygen in ether" doi="ethers"/>
-  <Type name="O_ald" class="O_sp2" element="O" mass="15.99940" def="O=[_HC]" desc="O in aldehyde" doi="ethers"/>
-  <Type name="O_ket" class="O_sp2" element="O" mass="15.99940" def="O=C([_CH3,_CH2,_HC,C])[_CH3,_CH2,_HC,C]" desc="O in ketone" doi="ethers"/>
+  <Type name="O_ald" class="O_sp2" element="O" mass="15.99940" def="O[_HC;X2]" desc="O in aldehyde" doi="ethers"/>
+  <Type name="O_ket" class="O_sp2" element="O" mass="15.99940" def="O[C;X3]([_CH3,_CH2,_HC,C])[_CH3,_CH2,_HC,C]" desc="O in ketone" 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"/>
@@ -84,10 +84,10 @@
   <Angle class1="CHx" type2="O" class3="H" angle="1.89368" k="460.62120"/>
   <!-- ethers -->
   <Angle class1="CHx" type2="O_eth" class3="CHx" angle="1.95477" k="502.19338"/>
-  <Angle class1="CHx" class2="CHx" type2="O_eth" angle="1.95477" k="!condme50300"/>
+  <Angle class1="CHx" class2="CHx" type3="O_eth" angle="1.95477" k="418.21733"/>
   <!-- aldehydes and ketones -->
-  <Angle class1="CHx" type2="C_ket" class3="CHx" angle="!117.2" k="!62500"/>
-  <Angle class1="CHx" class2="CHx" class3="O_sp2" angle="!121.4" k="!62500"/>
+  <Angle class1="CHx" type2="C_ket" class3="CHx" angle="2.04552" k="519.65389"/>
+  <Angle class1="CHx" class2="CHx" class3="O_sp2" angle="2.11883" k="519.65389"/>
  </HarmonicAngleForce>
  <RBTorsionForce>
   <!-- CHX-[CH2]-[CH2]-CHY -->
@@ -134,15 +134,15 @@
   <!-- CHX-[C]-[O]-H -->
   <Proper class1="CHx" type2="C_O" type3="O" class4="H" c0="1.35991" c1="4.07974" c2="0.0" c3="-5.43965" c4="0.0" c5="0.0"/>
   <!-- CHX-CHY-[O]-CHZ ether -->
-  <Proper class1="CHx" class2="CHx" class3="O_eth" class4="CHx" c0="0.0" c1="!725.35" c2="!-163.75" c3="!558.20" c4="0.0" c5="0.0"/>
+  <Proper class1="CHx" class2="CHx" class3="O_eth" class4="CHx" c0="7.94904" c1="7.89250" c2="2.72298" c3="-18.5645" c4="0.0" c5="0.0"/>
   <!-- CHX-[CH2]-[CH2]-[O] ether -->
-  <Proper class1="CHx" type2="CH2_sp3" type3="CH2_O" type4="O_eth" c0="0.0" c1="!176.62" c2="!-53.34" c3="!769.93" c4="0.0" c5="0.0"/>
-  <Proper class1="CHx" type2="CH2_Cald" type3="CH2_O" type4="O_eth" c0="0.0" c1="!176.62" c2="!-53.34" c3="!769.93" c4="0.0" c5="0.0"/>
+  <Proper class1="CHx" type2="CH2_sp3" type3="CH2_O" type4="O_eth" c0="6.98307" c1="17.7361" c2="0.88699" c3="-25.6062" c4="0.0" c5="0.0"/>
+  <Proper class1="CHx" type2="CH2_Cald" type3="CH2_O" type4="O_eth" c0="6.98307" c1="17.7361" c2="0.88699" c3="-25.6062" c4="0.0" c5="0.0"/>
   <!-- [O]-[CH2]-[CH2]-[O] ether -->
-  <Proper type1="O_eth" type2="CH2_O" type3="CH2_O" type4="O_eth" c0="!503.24" c1="0.0" c2="!-251.62" c3="!1006.47" c4="0.0" c5="0.0"/>
+  <Proper type1="O_eth" type2="CH2_O" type3="CH2_O" type4="O_eth" c0="8.36825" c1="25.1048" c2="4.18417" c3="-33.4730" c4="0.0" c5="0.0"/>
   <!-- CHX-CHY-[C]=[O] -->
-  <Proper class1="CHx" class2="CHx" type3="CH_ald" class4="O_sp2" c0="!2035.58" c1="!-736.9" c2="!57.84" c3="!-293.23" c4="0.0" c5="0.0"/>
-  <Proper class1="CHx" class2="CHx" type3="C_ket" class4="O_sp2" c0="!2035.58" c1="!-736.9" c2="!57.84" c3="!-293.23" c4="0.0" c5="0.0"/>
+  <Proper class1="CHx" class2="CHx" type3="CH_ald" class4="O_sp2" c0="9.32159" c1="-1.18722" c2="-0.96182" c3="9.7522" c4="0.0" c5="0.0"/>
+  <Proper class1="CHx" class2="CHx" type3="C_ket" class4="O_sp2" c0="9.32159" c1="-1.18722" c2="-0.96182" c3="9.7522" c4="0.0" c5="0.0"/>
   <!-- 
   No parameters for CHX-[CH2]-[CH]-OH, CHX-[CH2]-[C]-OH, CHX-[CH]-[CH2]-OH,
   CHX-[CH]-[CH]-OH, CHX-[CH]-[C]-OH, CHX-[C]-[CH2]-OH, CHX-[C]-[CH]-OH,
@@ -151,7 +151,7 @@
  </RBTorsionForce>
  <NonbondedForce coulomb14scale="0" lj14scale="0">
   <Atom type="O" charge="-0.700" sigma="0.302" epsilon="0.773245"/>
-  <Atom type="O_eth" charge="-0.500" sigma="0.28" epsilon="!conv!93.0"/>
+  <Atom type="O_eth" charge="-0.500" sigma="0.28" epsilon="0.457295"/>
   <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"/>
@@ -170,10 +170,10 @@
   <Atom type="C_sp3" charge="0.0" sigma="0.64" epsilon="0.00415723"/>
   <Atom type="C_eth" charge="0.25" sigma="0.58" epsilon="0.00415723"/>
   <Atom type="C_Cald" charge="-0.043" sigma="0.64" epsilon="0.00415723"/>
-  <Atom type="CH_ald" charge="0.525" sigma="0.352" epsilon="!convme!54.0"/>
-  <Atom type="C_ket" charge="0.424" sigma="0.382" epsilon="!convme!40.0"/>
-  <Atom type="O_ald" charge="-0.482" sigma="0.305" epsilon="!convme!79.0"/>
-  <Atom type="O_ket" charge="-0.424" sigma="0.305" epsilon="!convme!79.0"/>
+  <Atom type="CH_ald" charge="0.525" sigma="0.352" epsilon="0.448981"/>
+  <Atom type="C_ket" charge="0.424" sigma="0.382" epsilon="0.332578"/>
+  <Atom type="O_ald" charge="-0.482" sigma="0.305" epsilon="0.656842"/>
+  <Atom type="O_ket" charge="-0.424" sigma="0.305" epsilon="0.656842"/>
   <!--
   <Atom type="CH2_sp2" charge="0.0" sigma="0.3675" epsilon="0.706729"/>
   <Atom type="CH_sp2" charge="0.0" sigma="0.373" epsilon="0.390780"/>

foyer/trappe_validation/dimethylether/dme.mol2

@@ -4,9 +4,9 @@ DME
 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
+       1 _CH3        12.5360     1.0140    22.0490 CH3_eth       1 DME        0.265000
+       2 O           13.5570     1.3980    22.8620 O_eth         1 DME        0.000000
+       3 _CH3        13.5710     2.7160    23.1980 CH3_eth       1 DME        0.265000
 @<TRIPOS>BOND
        1        1        2 1
        2        2        3 1