[gmx-users] Carbon-Alpha RMSD Plots

jt555 jt555 at protonmail.com
Mon Apr 9 17:53:26 CEST 2018

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,


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