biowerkzeug

Hi all

I newly joined in this community, I am new to Molecular dynamics. I am interested in studying memebrane protein structure dynamics, I did downloaded HIPPO and run first time and it give me lot output files. I like to know how to intrepet the reslult and analysis. Also is their any standard input file for running md for membrane proteins in Hippo.

Thanks, really appreciated if someone direct me

venkat

Hi vkabs,

to answer your request for an standard input file: The HIPPO executable comes with a lot of test jobs. One of this jobs is an MD simulation with Generalized Born Implicit-Membrane (GBIM). May be the hippo_input.txt file is a good basis for setting up a new simulation by your self.

For a good interpretation of your simulation you should start with an analysis of the Energies over the time. You can find them in the "E.dat" and plot them e.g. with Gnuplot in Linux. HIPPO its self supports the RMSD- and the helicity-analysis. Just have a look in the manual at the last 4 pages for a short description how to use them.

I hope I could help you a bit.