[hisano]

Dear all,

In the tutorial 6.2, a 10 nsec simulation is calculated in the production job. However, Figure 15 (rmsd vs time) shows a period of 1 nsec. How can I make a rmsd figure with a period of 10 nsec?

(Even though I modified the rmsd.inp parameters md_step1, mdout_period1, and ana_period1, I couldn’t create a figure with time >1000 (ps). Log files of rmsd_analysis calculation indicated that calculation was terminated at the point “number of structure = 1000” and error messages were shown in the terminal. )

Best,

Tamao Hisano

[oshima]

Dear Hisano-san,

Thanks for informing the problem. It’s my mistake. I corrected Figure 15 and the script files in 4_analysis. Please use “plot.sh” to plot your results using gnuplot.

1000 is not time. It is the number of snapshots in run_prod.dcd. In this tutorial, snapshot is ouput every 4000 time steps (= 2.5 fs * 4000 = 10 ps). So, 1000 * 10 ps = 10 ns.

Best,

Hiraku Oshima

[hisano]

Dear Oshima-san,

I understand it is a matter of labeling and the plot is calculated for the 10-ns run. Thank you for the new version of the shell script.

Best,

Tamao Hisano