I do DPD simulations and when calculating the RDF, when I take the delta r value as 0.1, there are different peak heights when I get 0.01. Which delta r value would be better to use? rdpd = 4.48A
Hi Mr. Mohamed, your videos are really helpful, thanks. l am a new user MD simulation using LAMMPS packages, so I don't know how to plot Rg vs time for my trajectory file (using VMD tools). If you know about that and could be described it in a short video. I would be very appreciated it.
I do DPD simulations and when calculating the RDF, when I take the delta r value as 0.1, there are different peak heights when I get 0.01.
Which delta r value would be better to use?
rdpd = 4.48A
What if we use protein-ligand complex and calculate g(r) ligand from protein? It is valid?
Hi Mr. Mohamed, your videos are really helpful, thanks. l am a new user MD simulation using LAMMPS packages, so I don't know how to plot Rg vs time for my trajectory file (using VMD tools). If you know about that and could be described it in a short video. I would be very appreciated it.
Why use VMD? Use the MDAnalysis package because it is simple and straightforward
hello
How do you calculate rdf in vmd for membrane and drug?
Hello,
Is there any way of getting the RDF in VMD for a nonorthorhombic cell?
Thank you!
Hi thanks for the tutorial, but could it calculate rdf from a fixed coordinate? Like COM of the system?
Hi, Sir
How can we use the octahedron solvent box in VMD?
hi,good video sir.i have a small question how can i generate RDF plot from lammps trajectory file. ,
The same thing , if VMD can read lammps traj .
thank you for the suggestion sir. the same way i tried in the vmd but it is showing that the values of g(r) is zero. the curve becomes flatten..
sorry for the bother, but in your selection, you simply typed protein and water. how does VMD know what molecule you are referring to?
for any other new person, I had forgotten to also load the psf file.
you have to go over basic vmd tutorial
I have lammmps trajectory (.strj) file will it work?
You can try to load it VMD, it can handle wide range of file extensions let me know if it can deal with .strj cos I don't remeber
Hi, your video is really helpful!! Btw, do you know how to calculate the coordinate number from this rdf data? Thanks!!
no