Index: md/init.xyz
===================================================================
--- md/init.xyz	(revision 0)
+++ md/init.xyz	(revision 30)
@@ -0,0 +1,41 @@
+39
+Lattice="30.0 0.0 0.0 0.0 30.0 0.0 0.0 0.0 30.0" Properties=species:S:1:pos:R:3:momenta:R:3:Z:I:1 Pyrene_COOH_sec_amine=T pbc="F F F"
+C     -4.15654228       3.67480865       0.04852377       0.47824048       0.58971997       0.29142915        6 
+C     -4.57316847       3.21293954       1.28317742       0.37843364      -0.70690403      -1.58228631        6 
+C     -5.92050052       2.88816633       1.53542229       0.86982911      -1.24368327       0.77689428        6 
+C     -6.87744371       3.05538601       0.49021201      -1.57135917       0.28226827       0.95176798        6 
+C     -5.09389465       3.82550242      -0.99053823      -0.47736020      -0.15715462      -0.04810088        6 
+C     -6.44881092       3.50737316      -0.79399151      -0.75416193      -1.44443120      -0.71582209        6 
+C     -8.64339879       2.26763020       1.98402291       0.47489748      -1.06445359       1.32364106        6 
+C     -8.23776664       2.74434933       0.70624520      -1.19368259       0.84464831       0.15428858        6 
+C    -10.01162193       1.96244219       2.17200147      -0.72377672      -0.26840280      -0.34571388        6 
+C    -10.93846024       2.11983357       1.13933965      -0.96002778       0.26349195      -0.07289022        6 
+C    -10.52770164       2.59403193      -0.10936358      -1.35635031       1.99115444      -0.23903202        6 
+C     -9.18433373       2.87753631      -0.33743198      -2.18011447      -1.70782086       0.64356671        6 
+H     -3.83651654       3.04565663       2.17169764       0.11147076      -0.45480278       0.72645230        1 
+H     -4.73791409       4.20317701      -1.99553429       0.29087210       0.00272994      -0.18916988        1 
+H    -10.33810658       1.57096310       3.10145112       0.21179147      -0.41223370      -0.44543121        1 
+H    -11.95525086       1.87585383       1.35235665       0.25513421      -0.03917224       0.47114040        1 
+H    -11.26476689       2.60345922      -0.90425142       0.01310554      -0.71923826      -0.00385328        1 
+C     -7.70969361       2.13015458       3.01359758      -0.73509918       0.08539689       1.62699188        6 
+C     -6.36886324       2.43786114       2.76841636      -0.77234418      -0.30252545      -1.44799521        6 
+C     -8.74995347       3.33611629      -1.60525572      -2.22266842      -1.51543162      -1.43962707        6 
+C     -7.38126248       3.64363206      -1.82177371       0.75694506      -1.45522124      -1.37782364        6 
+H     -9.41216649       3.46275759      -2.41289603       0.28212925      -0.19975490      -0.00896751        1 
+H     -7.07561012       4.05112738      -2.83924724       0.07497293       0.29919291      -0.42197101        1 
+H     -7.96896389       1.73342085       4.03982587       0.35513866      -0.36637519       0.58573890        1 
+H     -5.63929936       2.31156606       3.56852322       0.19230828       0.01409492      -0.23090060        1 
+C     -2.70355064       3.98501696      -0.15187111       1.19594359      -0.53225946      -1.72185890        6 
+O     -1.83562800       3.87433124       0.71526906       2.00815970      -0.27143817       0.43757568        8 
+O     -2.44525243       4.43623465      -1.38477544      -1.43337701       2.91598172      -0.86188633        8 
+H     -1.31504813       4.61356712      -1.37802865       0.65847853       0.32553394      -0.12515302        1 
+N      0.91463075       4.01993269      -0.13263765      -0.76644445       0.74439402       1.73852400        7 
+C      0.41719583       4.99002636       0.80090975       0.51282545      -0.72703496       0.55701750        6 
+H      0.77720297       6.01422310       0.46544888       0.34743439       0.07984177      -0.29708936        1 
+H      0.80544295       4.80778494       1.82510874      -0.10749731       0.07663135       0.11127747        1 
+H     -0.64527946       5.00068239       0.85743724       0.34207353       0.04895572       0.15314204        1 
+C      0.49872316       2.67658905       0.22066911      -0.22054367       0.32144257       0.09906241        6 
+H      0.46945902       4.26227112      -1.13069538      -0.51714704       0.04235940      -0.36745482        1 
+H     -0.59696152       2.57917335       0.23952273      -0.27461320       0.04516885      -0.03311572        1 
+H      0.91630403       2.40134844       1.25616912       0.04839192       0.22881788       0.44641178        1 
+H      0.89783668       1.93453982      -0.50992874      -0.00927107      -0.07071277       0.06117916        1 
