Dear all,
I am trying to run the tests for lmode in amber11 and after many
different approaches: I could not get the correct results.
These are the results that I have when I run the vancomycin_lmod test:
As it can be seen, I have wrong results for the Energies.
I did the calculation with amber10 and I had " qualitatively similar results" .
If I run the lmod test with the XMIN option: it works !!
Any idea to solve this problem ?
>>>
>>> 4,10c4,10
>>> < 1 E = -127.997 ( 0.091) Rg = 2.090
>>> < 1 /10 E = -126.921 ( 0.099) Rg = 1.915 rmsd= 3.993 p= 0.4880
>>> < 1 / 6 E = -123.890 ( 0.100) Rg = 2.310 rmsd= 2.856 p= 0.0647
>>> < 7 / 4 E = -105.723 ( 0.096) Rg = 1.971 rmsd= 1.575 p= 0.
>>> < 7 / 7 E = -125.540 ( 0.095) Rg = 2.176 rmsd= 1.016 p= 0.1943
>>> < 10 / 6 E = -110.778 ( 0.089) Rg = 2.305 rmsd= 1.491 p= 0.
>>> < 10 / 4 E = -127.300 ( 0.096) Rg = 1.980 rmsd= 1.150 p= 0.6283
>>> ---
>>> > 1 E = 0. ( 0.094) Rg = 2.105
>>> > 1 /20 E = 0. ( 0.090) Rg = 2.127 rmsd= 2.704 p= 1.0000
>>> > 1 /20 E = 0. ( 0.091) Rg = 2.341 rmsd= 4.422 p= 1.0000
>>> > 7 /20 E = 0. ( 0.089) Rg = 5.348 rmsd= 8.991 p= 1.0000
>>> > 7 /20 E = 0. ( 0.088) Rg = 1.984 rmsd= 4.253 p= 1.0000
>>> > 10 /20 E = 0. ( 0.087) Rg = 2.151 rmsd= 2.330 p= 1.0000
>>> > 10 /20 E = 0. ( 0.086) Rg = 2.028 rmsd= 1.442 p= 1.0000
>>> 12,18c12,18
>>> < 2 E = -126.921 ( 0.099) Rg = 1.915
>>> < 4 / 6 E = -166.552 ( 0.088) Rg = 1.940 rmsd= 1.654 p= 1.0000
>>> < 4 / 7 E = -132.830 ( 0.090) Rg = 2.167 rmsd= 1.649 p= 1.0000
>>> < 6 / 2 E = -139.924 ( 0.092) Rg = 1.910 rmsd= 1.373 p= 1.0000
>>> < 6 / 8 E = -127.098 ( 0.098) Rg = 1.957 rmsd= 1.593 p= 1.0000
>>> < 7 / 6 E = -98.455 ( 0.096) Rg = 2.141 rmsd= 2.752 p= 0.
>>> < 7 / 4 E = -125.520 ( 0.092) Rg = 1.945 rmsd= 1.090 p= 0.3930
>>> ---
>>> > 2 E = 0. ( 0.090) Rg = 2.127
>>> > 4 /20 E = 0. ( 0.096) Rg = 3.604 rmsd= 5.061 p= 1.0000
>>> > 4 /20 E = 0. ( 0.097) Rg = 2.006 rmsd= 4.016 p= 1.0000
>>> > 8 /20 E = 0. ( 0.092) Rg = 2.121 rmsd= 1.966 p= 1.0000
>>> > 8 /20 E = 0. ( 0.098) Rg = 1.913 rmsd= 2.589 p= 1.0000
>>> > 10 /20 E = 0. ( 0.099) Rg = 1.913 rmsd= 3.637 p= 1.0000
>>> > 10 /20 E = 0. ( 0.089) Rg = 3.257 rmsd= 4.392 p= 1.0000
>>> 21,27c21,33
>>> < 1 E = -166.552 / 2 Rg = 1.940
>>> < 2 E = -132.830 / 1 Rg = 2.167
>>> < 3 E = -127.997 / 2 Rg = 2.090
>>> < 4 E = -127.098 / 2 Rg = 1.957
>>> < 5 E = -125.540 / 1 Rg = 2.176
>>> < 6 E = -125.520 / 1 Rg = 1.945
>>> < 7 E = -123.890 / 1 Rg = 2.310
>>> ---
>>> > 1 E = 0. / 1 Rg = 3.257
>>> > 2 E = 0. / 1 Rg = 1.913
>>> > 3 E = 0. / 1 Rg = 1.913
>>> > 4 E = 0. / 1 Rg = 2.121
>>> > 5 E = 0. / 1 Rg = 2.006
>>> > 6 E = 0. / 1 Rg = 3.604
>>> > 7 E = 0. / 1 Rg = 2.028
>>> > 8 E = 0. / 1 Rg = 2.151
>>> > 9 E = 0. / 1 Rg = 1.984
>>> > 10 E = 0. / 1 Rg = 5.348
>>> > 11 E = 0. / 1 Rg = 2.341
>>> > 12 E = 0. / 1 Rg = 2.127
>>> > 13 E = 0. / 1 Rg = 2.105
>>
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Received on Wed Apr 25 2012 - 11:30:02 PDT
