[gmx-users] 1-D free energy plots using g_sham

[Mark Abraham]

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
>
> --
> 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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>