I ran a gromacs MD simulation of the 5 resi peptide for 1ns, I want to pick up a low energy structure from the trajectory, how could I determine what is the energy for each of the structure in the trajectory? Is there a particular command that I can use to get the frame number with corresponding energy value?
Hi
There are several ways; Follow the bellow tutorial For the easiest way. Plot the free energy surface and take the lowest energy structure.
http://www.strodel.info/index_files/lecture/html/analysis-10.html
Krishnendu Bera Thanks for the link! It is really helpful! I followed the instruction successfully for the first three steps and generated the free energy plot with python script.
However in the fourth step ( awk ' {if ( ($1 > 0.77 ) && ($1 < 0.78 ) && ($2 > 0.75) && ($2 < 0.76)) print "Frame: ", NR-1,$1,$2}' rgyr_rmsd.dat > energy_min1.dat ), the energy_min1.dat file generated is an empty file, I am not sure what happened. Should I change the numbers in the command?
In the free energy plot generated from step three , there are points with low Gibbs free energy value, if the fourth step command does not work, could I just pick the low energy structure from the plot?
In addition, There is a command "gmx energy -f md.edr -o potential.xvg" that can generate a xvg file with energy for each time frame during the simulation, could I pick the low energy structure from there?
$1 is the row which represents the Rgyr values and $2 represents the R.M.S.D values. You have to look inside the rgyr-rmd.dat file. Then select the cut-off values accordingly. Example, If Rgyr is 2 to 2.5 nm, then the value may be ($1 > 2.3 ) && ($1 < 2.4), similarly rmsd is 0.1 to 0.7 nm, then ($2 > 0.5) && ($2 < 0.55) and so on.
Hope it will help.
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