RMSD in membrane protein simulation

Question

[a.raaj000]

Hello,

I am working on membrane protein with residue around 1300. I had completed a 6ns-extended simulation. I am facing a problem in plotting RMSD for protein. I extended my simulation each 1 ns step, so there is six trajectory file which is combined using trjcat.

trjcat -f step1.trr step2.trr step3.trr step4.trr step5.trr step6.trr -o fixed.trr

Now using g_rms command when I am plotting the graph, it is coming something strange which I am attaching below. I am unable to understand the reason of this kind of plot.

Please suggest the problem behind this.

Thanks

[João Rodrigues]

Following your comment and the g_rms input command, it seems you are using a structure from step6 as a reference, which could explain this plot. I would plot the rmsd plot against the initial structure, to see if your simulation doesn't have jumps because of all the extensions.

[a.raaj000]

Thanks sir. I used the initial structure for reference. Now, the plot is nice.

[João Rodrigues]

It doesn't necessarily have to be the initial structure. You can (and should) use other structures if it makes sense to answer a particular question. I don't know how and what you are doing, but you can find some hints on how to analyze MD trajectories and particularly, quality control, in this website.

Answer 1

[João Rodrigues]

What is the reference structure you are using to calculate the RMSD? It would seem you used not the initial structure but something else that matches that particular frame. What was the command you used for the g_rms calculation?

Answer 2

[a.raaj000]

The g_rms command which I am using is

g_rms -f fixed.trr -s step6.tpr -n index.ndx -o rmsd.xvg

So, for reference structure, whether I have to use the structure present before starting production MD or the initial structure before starting simulation process?

And, Thanks for your suggestion and help.

[João Rodrigues]

You should reply to my answer with a comment and/or edit your initial post.