I have simulated the protein in water and 2) protein with ligand
now I want to check the g energy in gromacs for both system individually and then combine to one plot. How could I do this?
You will need to run g_energy command separately on both the .edr files, which will generate two plots in .xvg format. Then while visualizing the .xvg graph, you can view individual graph also and combine both in a one plot also.
for individual, use command: xmgrace energy1.xvg
for combined: xmgrace energy1.xvg energy2.xvg
and then you can save this combined plot.
g_energy -f protein_npt.edr -n index.ndx -o Eng.xvg
(As an example)
Now see the plot in xmgrace as
xmgrace Eng.xvg -free
Thanku so much for answers,
but how can i calculate the the g_energy after final md run for the system ?
After any run, whether it is equilibration and or production, you will have a file with extension '.edr'. Extract any energy term from there by the aforementioned protocol.
Like following the example and using this command no edr file is there, edr files are generated for pressure and temperature only
grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr
With grompp, you are not performing a simulation run, you just generate the input file for the simulation. So proceed by running e.g.
mdrun -s md_0_1.tpr -deffnm md_out
and you will get a "md_out.edr" file for your simulation run, which you can then analyze with g_energy.
Follow this tutorial to understand the basic workflow of setting up a MD simulation in Gromacs and performing analysis of the trajectories: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ ... and read the manual. Gromacs has a very well written manual.
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