[gmx-users] Carbon-Alpha RMSD Plots

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 9 18:54:36 CEST 2018


The header in your xvg file confirms how you ran the analysis, and your
simulation .log file confirms what you actually did. As does gmx check on
your trajectory file.


On Mon, Apr 9, 2018, 17:53 jt555 <jt555 at protonmail.com> wrote:

> Hello there,
> I am writing to seek clarification regarding the following:
> I use GROMACS version 5.1.2 and Grace (xmgrace) version 5.1.25
> I ran a molecular dynamics simulation for 1 microsecond (~ 1055 ns). I
> used xmgrace to plot a carbon-alpha RMSD plot and I noticed that the x-axis
> [Time (picoseconds)] is suggestive of the fact that the total simulation
> time was 1e+09 picoseconds (1000 microseconds). Furthermore, invocation of
> gmx rms did not involve the option -tu, therefore it was set to default
> (i.e., picoseconds). I discarded the initial portion to equilibration (250
> ns). The question I have is if I considered the values in femtoseconds then
> the RMSD plot as it appears makes absolute sense, however the x-axis is
> clearly set in picoseconds.
> I thank you for your kind assistance.
> Yours faithfully,
> JT
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