[gmx-users] 1-D free energy plots using g_sham
Mark Abraham
mark.j.abraham at gmail.com
Fri Apr 4 09:00:59 CEST 2014
You've discarded the legend in the header of the file...
Mark
On Apr 4, 2014 8:17 AM, "richa" <richa.s.rathorerr at gmail.com> wrote:
> 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
>
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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