diff --git a/tools/msi2lmp/test/reference/h2-h2o-class1.data b/tools/msi2lmp/test/reference/h2-h2o-class1.data
index 56b213268..8bed626c7 100644
--- a/tools/msi2lmp/test/reference/h2-h2o-class1.data
+++ b/tools/msi2lmp/test/reference/h2-h2o-class1.data
@@ -1,55 +1,55 @@
LAMMPS data file from msi2lmp v3.8 for h2-h2o-class1
5 atoms
3 bonds
1 angles
0 dihedrals
0 impropers
3 atom types
2 bond types
1 angle types
- 0.000000000 10.000000000 xlo xhi
- 0.000000000 10.000000000 ylo yhi
- 0.000000000 10.000000000 zlo zhi
+ -0.200000000 9.800000000 xlo xhi
+ -0.200000000 9.800000000 ylo yhi
+ 0.500000000 10.500000000 zlo zhi
Masses
1 1.007970
2 15.999400
3 1.007970
Pair Coeffs
1 0.0380000011 2.4499714540
2 0.1520725945 3.1506561105
3 0.0000000000 0.0000000000
Bond Coeffs
1 398.7500 0.7461
2 540.6336 0.9570
Angle Coeffs
1 50.0000 104.5200
Atoms
1 1 1 0.000000 4.600000000 5.000000000 2.500000000
2 1 1 0.000000 5.400000000 5.000000000 2.500000000
3 2 2 -0.834000 5.000000000 5.000000000 7.500000000
4 2 3 0.417000 4.000000000 5.000000000 7.500000000
5 2 3 0.417000 5.000000000 4.000000000 7.500000000
Bonds
1 1 1 2
2 2 3 4
3 2 3 5
Angles
1 1 4 3 5
diff --git a/tools/msi2lmp/test/reference/h2-h2o-class1.data2 b/tools/msi2lmp/test/reference/h2-h2o-class1.data2
index 76bec31e5..8ed4eb089 100644
--- a/tools/msi2lmp/test/reference/h2-h2o-class1.data2
+++ b/tools/msi2lmp/test/reference/h2-h2o-class1.data2
@@ -1,59 +1,59 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 19
5 atoms
3 atom types
3 bonds
2 bond types
1 angles
1 angle types
-0.0000000000000000e+00 1.0000000000000000e+01 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
-0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi
+-2.0000000000000001e-01 9.8000000000000007e+00 xlo xhi
+-2.0000000000000001e-01 9.8000000000000007e+00 ylo yhi
+5.0000000000000000e-01 1.0500000000000000e+01 zlo zhi
Masses
1 1.00797
2 15.9994
3 1.00797
Pair Coeffs
1 0.038 2.44997
2 0.152073 3.15066
3 0 0
Bond Coeffs
1 398.75 0.7461
2 540.634 0.957
Angle Coeffs
1 50 104.52
Atoms
1 1 1 0.0000000000000000e+00 4.6277675306507575e+00 4.9999986371834391e+00 2.5000000000000000e+00 0 0 0
2 1 1 0.0000000000000000e+00 5.3722298760660010e+00 4.9999986512903849e+00 2.5000000000000000e+00 0 0 0
3 2 2 -8.3399999999999996e-01 4.9248756348400917e+00 4.9248756919813266e+00 7.5000000000000000e+00 0 0 0
4 2 3 4.1699999999999998e-01 3.9757012788791712e+00 5.0994256861724345e+00 7.5000000000000000e+00 0 0 0
5 2 3 4.1699999999999998e-01 5.0994256795639785e+00 3.9757013333724149e+00 7.5000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 3 4
3 2 3 5
Angles
1 1 4 3 5
diff --git a/tools/msi2lmp/test/reference/h2-h2o-class2b.data b/tools/msi2lmp/test/reference/h2-h2o-class2b.data
index 82457b8f7..354761764 100644
--- a/tools/msi2lmp/test/reference/h2-h2o-class2b.data
+++ b/tools/msi2lmp/test/reference/h2-h2o-class2b.data
@@ -1,63 +1,63 @@
LAMMPS data file from msi2lmp v3.8 for h2-h2o-class2b
5 atoms
3 bonds
1 angles
0 dihedrals
0 impropers
3 atom types
2 bond types
1 angle types
- 0.000000000 10.000000000 xlo xhi
- 0.000000000 10.000000000 ylo yhi
- 0.000000000 10.000000000 zlo zhi
+ -0.200000000 9.800000000 xlo xhi
+ -0.200000000 9.800000000 ylo yhi
+ -0.500000000 9.500000000 zlo zhi
Masses
1 15.999400
2 1.007970
3 1.007970
Pair Coeffs
1 0.2740000000 3.6080000000
2 0.0130000000 1.0980000000
3 0.0200000000 2.9950000000
Bond Coeffs
1 0.9700 563.2800 -1428.2200 1902.1200
2 0.7414 414.0000 0.0000 0.0000
Angle Coeffs
1 103.7000 49.8400 -11.6000 -8.0000
BondBond Coeffs
1 -9.5000 0.9700 0.9700
BondAngle Coeffs
1 22.3500 22.3500 0.9700 0.9700
Atoms
1 2 1 -0.834000 5.000000000 5.000000000 2.500000000
2 2 2 0.417000 4.000000000 5.000000000 2.500000000
3 2 2 0.417000 5.000000000 4.000000000 2.500000000
4 1 3 0.000000 4.600000000 5.000000000 7.500000000
5 1 3 0.000000 5.400000000 5.000000000 7.500000000
Bonds
1 1 1 2
2 1 1 3
3 2 4 5
Angles
1 1 2 1 3
diff --git a/tools/msi2lmp/test/reference/h2-h2o-class2b.data2 b/tools/msi2lmp/test/reference/h2-h2o-class2b.data2
index a6faaeee9..1e3997455 100644
--- a/tools/msi2lmp/test/reference/h2-h2o-class2b.data2
+++ b/tools/msi2lmp/test/reference/h2-h2o-class2b.data2
@@ -1,67 +1,67 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 15
5 atoms
3 atom types
3 bonds
2 bond types
1 angles
1 angle types
-0.0000000000000000e+00 1.0000000000000000e+01 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
-0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi
+-2.0000000000000001e-01 9.8000000000000007e+00 xlo xhi
+-2.0000000000000001e-01 9.8000000000000007e+00 ylo yhi
+-5.0000000000000000e-01 9.5000000000000000e+00 zlo zhi
Masses
1 15.9994
2 1.00797
3 1.00797
Pair Coeffs
1 0.274 3.608
2 0.013 1.098
3 0.02 2.995
Bond Coeffs
1 0.97 563.28 -1428.22 1902.12
2 0.7414 414 0 0
Angle Coeffs
1 103.7 49.84 -11.6 -8
BondBond Coeffs
1 -9.5 0.97 0.97
BondAngle Coeffs
1 22.35 22.35 0.97 0.97
Atoms
1 2 1 -8.3399999999999996e-01 4.9326604874206312e+00 4.9326605407695370e+00 2.5000000000000000e+00 0 0 0
2 2 2 4.1699999999999998e-01 3.9718089676777457e+00 5.0955333693623475e+00 2.5000000000000000e+00 0 0 0
3 2 2 4.1699999999999998e-01 5.0955333627272008e+00 3.9718090160698245e+00 2.5000000000000000e+00 0 0 0
4 1 3 0.0000000000000000e+00 4.6314953143112261e+00 4.9999985334767372e+00 7.5000000000000000e+00 0 0 0
5 1 3 0.0000000000000000e+00 5.3685018678631966e+00 4.9999985403215526e+00 7.5000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 1 1 3
3 2 4 5
Angles
1 1 2 1 3
diff --git a/tools/msi2lmp/test/reference/water-class1.data b/tools/msi2lmp/test/reference/water-class1.data
index a88401916..2ace6b692 100644
--- a/tools/msi2lmp/test/reference/water-class1.data
+++ b/tools/msi2lmp/test/reference/water-class1.data
@@ -1,49 +1,49 @@
LAMMPS data file from msi2lmp v3.8 for water-class1
3 atoms
2 bonds
1 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
- 0.000000000 10.000000000 xlo xhi
- 0.000000000 10.000000000 ylo yhi
+ -0.333333333 9.666666667 xlo xhi
+ -0.333333333 9.666666667 ylo yhi
0.000000000 10.000000000 zlo zhi
Masses
1 15.999400
2 1.007970
Pair Coeffs
1 0.1520725945 3.1506561105
2 0.0000000000 0.0000000000
Bond Coeffs
1 540.6336 0.9570
Angle Coeffs
1 50.0000 104.5200
Atoms
1 1 1 -0.834000 5.000000000 5.000000000 5.000000000
2 1 2 0.417000 4.000000000 5.000000000 5.000000000
3 1 2 0.417000 5.000000000 4.000000000 5.000000000
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
diff --git a/tools/msi2lmp/test/reference/water-class1.data2 b/tools/msi2lmp/test/reference/water-class1.data2
index ff815993a..fed942ccf 100644
--- a/tools/msi2lmp/test/reference/water-class1.data2
+++ b/tools/msi2lmp/test/reference/water-class1.data2
@@ -1,51 +1,51 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 21
3 atoms
2 atom types
2 bonds
1 bond types
1 angles
1 angle types
-0.0000000000000000e+00 1.0000000000000000e+01 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
+-3.3333333300000001e-01 9.6666666669999994e+00 xlo xhi
+-3.3333333300000001e-01 9.6666666669999994e+00 ylo yhi
0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi
Masses
1 15.9994
2 1.00797
Pair Coeffs
1 0.152073 3.15066
2 0 0
Bond Coeffs
1 540.634 0.957
Angle Coeffs
1 50 104.52
Atoms
1 1 1 -8.3399999999999996e-01 4.9243617135708035e+00 4.9243617135708035e+00 5.0000000000000000e+00 0 0 0
2 1 2 4.1699999999999998e-01 3.9759569645562172e+00 5.0996813218729828e+00 5.0000000000000000e+00 0 0 0
3 1 2 4.1699999999999998e-01 5.0996813218729828e+00 3.9759569645562172e+00 5.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
diff --git a/tools/msi2lmp/test/reference/water-class2b.data b/tools/msi2lmp/test/reference/water-class2b.data
index a2dfe721a..3092bad2a 100644
--- a/tools/msi2lmp/test/reference/water-class2b.data
+++ b/tools/msi2lmp/test/reference/water-class2b.data
@@ -1,57 +1,57 @@
LAMMPS data file from msi2lmp v3.8 for water-class2b
3 atoms
2 bonds
1 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
- 0.000000000 10.000000000 xlo xhi
- 0.000000000 10.000000000 ylo yhi
+ -0.333333333 9.666666667 xlo xhi
+ -0.333333333 9.666666667 ylo yhi
0.000000000 10.000000000 zlo zhi
Masses
1 15.999400
2 1.007970
Pair Coeffs
1 0.2740000000 3.6080000000
2 0.0130000000 1.0980000000
Bond Coeffs
1 0.9700 563.2800 -1428.2200 1902.1200
Angle Coeffs
1 103.7000 49.8400 -11.6000 -8.0000
BondBond Coeffs
1 -9.5000 0.9700 0.9700
BondAngle Coeffs
1 22.3500 22.3500 0.9700 0.9700
Atoms
1 1 1 -0.834000 5.000000000 5.000000000 5.000000000
2 1 2 0.417000 4.000000000 5.000000000 5.000000000
3 1 2 0.417000 5.000000000 4.000000000 5.000000000
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
diff --git a/tools/msi2lmp/test/reference/water-class2b.data2 b/tools/msi2lmp/test/reference/water-class2b.data2
index 3892a0f12..b24c1dd78 100644
--- a/tools/msi2lmp/test/reference/water-class2b.data2
+++ b/tools/msi2lmp/test/reference/water-class2b.data2
@@ -1,59 +1,59 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 15
3 atoms
2 atom types
2 bonds
1 bond types
1 angles
1 angle types
-0.0000000000000000e+00 1.0000000000000000e+01 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
+-3.3333333300000001e-01 9.6666666669999994e+00 xlo xhi
+-3.3333333300000001e-01 9.6666666669999994e+00 ylo yhi
0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi
Masses
1 15.9994
2 1.00797
Pair Coeffs
1 0.274 3.608
2 0.013 1.098
Bond Coeffs
1 0.97 563.28 -1428.22 1902.12
Angle Coeffs
1 103.7 49.84 -11.6 -8
BondBond Coeffs
1 -9.5 0.97 0.97
BondAngle Coeffs
1 22.35 22.35 0.97 0.97
Atoms
1 1 1 -8.3399999999999996e-01 4.9325083652589568e+00 4.9325083652589568e+00 5.0000000000000000e+00 0 0 0
2 1 2 4.1699999999999998e-01 3.9718836387945160e+00 5.0956079959465290e+00 5.0000000000000000e+00 0 0 0
3 1 2 4.1699999999999998e-01 5.0956079959465290e+00 3.9718836387945160e+00 5.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3