[gmx-users] Error problem in free energy calculation

Jianhui Tian jianhuitian at gmail.com
Tue Jul 22 21:11:31 CEST 2008


I have been trying to follow the tutorial
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial by
David Mobley to reproduce the solvation energy for methane in water. I
followed the instructions and got the solvation energy in good agreement
with the answer in the tutorial. But I noticed that the fluctuation for
every dgdl is very large. The numbers are attatched below. I have read the
thread in the mailling list about the error thing:
http://www.gromacs.org/pipermail/gmx-users/2007-May/027333.html   and
http://www.gromacs.org/pipermail/gmx-users/2007-May/027237.html, but still I
am very confused about the error and fluctuation. If the fluctuation is so
large, how well can we trust the solvation energy we got? Thanks a lot in
advance for your comment.

lambda    dgdl      fluctuation
0.0       4.713   11.426
0.1       2.209   13.584
0.2       0.534    14.920
0.3       -1.333   16.274
0.4       -3.944    18.264
0.5       -7.992    21.191
0.6       -17.773  27.100
0.7      -28.915   25.747
0.8      -24.6079  14.5232
0.9      -11.135    7.6318
1.0      -0.0948    4.337

Biocomputation and bioinformatics
Department of Physics
Rensselaer Polytechnic Institute
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