I would like to extract a structure from a GROMACS simulation at the timepoint corresponding to when the peptide is at its highest radius of gyration. Is there a way to do this without having to plot Rg and eyeballing the corresponding timepoint?
Thanks!
Write a simple script that parses the time series to find the maximum value and print out the corresponding time. Then use trjconv -dump to write out the exact frame. No eyeballing necessary.
Write a simple script that parses the time series to find the maximum value and print out the corresponding time. Then use trjconv -dump to write out the exact frame. No eyeballing necessary.
I use R to find it.
#Find the time with the highest radius of gyration
gyrate = read.table("gyrate.xvg",skip = 27)
max_radius = max(gyrate$V2)
time = gyrate$V1[which(gyrate$V2 == max(gyrate$V2))]
paste("The time with highest radius of gyration (",max_radius,") is: ", time,".",sep="")
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