Hello everyone,
I am brand new to any molecular dyanmics simulations and am having a difficult time viewing the RMSD results of my MD simulation. What I did for the experiment is I used the QwikMD tool in VMD to modify a residue of our protein, then I planned on observing the RMSD over the time of the simulation. When the simulation finished, I loaded the .qwikmd file into VMD. This file contains the initial structure of the protein, as well as all the .dcd files associated with the simulation. I can view how the backbone changes over time by either using the RMSD Trajectory Tool or the "Easy Run" tab of QwikMD. In both cases, I align the structures to the reference structure and can get it to output a reasonable RMSD for the whole backbone over time. However, whenever I try to tell it to plot the RMSD of the specific amino acid, I get one of two results: either an error message or a plot that shows RMSDs of the amino acid around 40. I figure the RMSD value of 40 cannot be correct because when I calculate the distance between the alpha carbons of the residue in the initial and final structure, there is only about a 2 Å difference.
I have spent all week trying to troubleshoot this and have looked for answers in nearly every single webpage on the subject, but none seem to fix this issue. I have also read the user manuals and VMD mailing list without any luck. My questions for you are:
1) Is it safe to assume something is wrong based on the fact that there is little difference in distance between the two alpha carbons but the RMSDs I am getting are much higher?
2) Could you please walk me through how to correctly specify which amino acid/atom to use and how to specify the reference structure? I believe I am selecting the reference structure correctly, but this could be the issue. I should note that I have tried specifying the atom by using "name CA and resid 53" but that tells me there is a change of 0 RMSD over time.
Thank you in advance for your time.
Make sure you correct for PBCs. Then align the structure. The easiest in VMD is: Extensions -> Analysis -> RMSD (there are three options). You can choose how to align the structure and on what to perform the RMSD for each of them.
Dear Nolan,
Please go through below link and try Ioana's reply also.
http://azevedolab.net/resources/MolegroVirtualDockerManual.pdf
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