hippo analysis the result

Discuss methods to obtain meaningful observables from simulation trajectories. You can share scripts or just ideas and links to other communities are very welcome, too. For Hippo-specific analysis have a look at the Hippo -> Analysis forum.
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vkabs
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Joined: Tue Feb 17, 2009 11:33 pm
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hippo analysis the result

Post by vkabs » Wed Feb 18, 2009 3:08 pm

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

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am
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Re: hippo analysis the result

Post by m.kalavera » Wed Feb 25, 2009 1:21 pm

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.

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