[gmx-users] g_energy & graph .xvg

[Carla Jamous]

Thank you all,

the xmgrace -nxy
worked.

but you're right, it's more useful to see the fluctuations.

Thanks
Carla

On Tue, Jun 1, 2010 at 10:02 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> Mark Abraham skrev:
>
>  ----- Original Message -----
>> From: Carla Jamous <carlajamous at gmail.com>
>> Date: Tuesday, June 1, 2010 17:48
>> Subject: [gmx-users] g_energy & graph .xvg
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>>
>>
>>> Hi everyone, please  I have a practical question that may sound stupid
>>> but I can't figure out the answer.
>>>
>>> When I run g_energy I type the Energies I need, for example:
>>> 10 (Potential)
>>> 14 (Kinetic)
>>>
>>>
>>>
>> 12 (Total)
>>
>>
>>>  My problem is even though I get the averages of the 3 energies on my
>>> screen, I can't get the three energies on the same graph (.xvg file).
>>>
>>>
>>
>> Well they have wildly different values, so plotting all three together
>> means you can't see any fluctuations, so you might as well just look at the
>> averages... If you want all three with fluctuations, then you'll need to
>> play with the plotting program's functionality for representations and axes
>> (for xmgrace). See
>> http://www.gromacs.org/Documentation/How-tos/Graphing_Data for various
>> ideas on plotting.
>>
>> Mark
>>
>>
> Zooming is of course an option. I for one find it helpful to inspect the
> energies as a function of time to get an idea of the convergence time for
> certain properties and to detect any wierdness in my setup that may have
> ruined my simulations.
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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