[gmx-users] 1-D free energy plots using g_sham
richa
richa.s.rathorerr at gmail.com
Fri Apr 4 08:11:46 CEST 2014
Hi all,
I wanted to know, if we can plot one dimensional free energy surfaces along
the dihedral angles (or any other variable) of alanine di peptide using
g_sham utility of gromacs.
Although I have already tried to plot the 1-D FES, using the command:
g_sham -f file.xvg -dist ener.xvg -notime
I'm not able to interpret the output file (ener.xvg) properly. What do the
columns of the file signify?
0 6.64884e+00 0.00000e+00 1.18886e+01
1 7.31465e+00 0.00000e+00 1.12228e+01
2 1.01060e+01 0.00000e+00 8.43147e+00
3 1.32323e+01 0.00000e+00 5.30516e+00
4 1.37136e+01 0.00000e+00 4.82386e+00
5 1.62660e+01 0.00000e+00 2.27146e+00
6 1.85375e+01 0.00000e+00 9.53674e-07
7 1.75323e+01 0.00000e+00 1.00514e+00
8 1.43114e+01 0.00000e+00 4.22602e+00
9 1.51009e+01 0.00000e+00 3.43658e+00
10 9.65403e+00 0.00000e+00 8.88344e+00
11 6.27844e+00 0.00000e+00 1.22590e+01
12 3.88477e+00 0.00000e+00 1.46527e+01
13 2.41910e+00 0.00000e+00 1.61184e+01
14 1.91590e+00 0.00000e+00 1.66216e+01
15 2.32423e+00 0.00000e+00 1.62132e+01
16 2.99187e+00 0.00000e+00 1.55456e+01
17 3.33564e+00 0.00000e+00 1.52018e+01
18 3.99115e+00 0.00000e+00 1.45463e+01
19 4.44382e+00 0.00000e+00 1.40936e+01
20 5.44056e+00 0.00000e+00 1.30969e+01
21 6.47099e+00 0.00000e+00 1.20665e+01
22 6.75345e+00 0.00000e+00 1.17840e+01
23 6.88511e+00 0.00000e+00 1.16524e+01
24 5.56308e+00 0.00000e+00 1.29744e+01
25 3.62964e+00 0.00000e+00 1.49078e+01
26 2.01501e+00 0.00000e+00 1.65225e+01
27 6.61140e-01 0.00000e+00 1.78763e+01
28 0.00000e+00 0.00000e+00 1.85375e+01
29 2.11306e-01 0.00000e+00 1.83262e+01
30 1.56937e+00 0.00000e+00 1.69681e+01
31 4.86484e+00 0.00000e+00 1.36726e+01
If not g_sham, is there any other utility that we can use to get the 1
dimensional free energy plots along different variables?
Thanks in advance
Richa
--
View this message in context: http://gromacs.5086.x6.nabble.com/1-D-free-energy-plots-using-g-sham-tp5015633.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
More information about the gromacs.org_gmx-users
mailing list