[gmx-users] g_energy & graph .xvg
erikm at xray.bmc.uu.se
Tue Jun 1 10:02:19 CEST 2010
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.
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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