Transrotscan: How to use it correctly ?

After a successful calculation you want more than just to see the atoms wiggle: Here you can discuss how to use Hippo to compute observables from the simulation. For more general discussions on analysis of simulations see also the Molecular Simulations -> Analysis forum.
Post Reply
m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Transrotscan: How to use it correctly ?

Post by m.kalavera » Wed May 06, 2009 9:53 am

Hello,
after a successful MC run, I used the transrot function in Hippo and know some simple questions came up to understand and make it use correctly.

How I used it : I created a new folder, copied the hippo executable, oplsa forcefield, movie.pdb and the used hippo_input.txt in it. Afterwards I just changed the mode in the hippo_input.txt into "transrot scan" and started hippo again.

The recieved output: I got a direct output in my terminal and 3 separate files
  • e_z_movie.dat
    e_z_theta_matrix_movie.dat
    e_z_theta_movie.dat
Both movie.dat files include the entry E-Einf. What does it mean ?
I have read your publication in which you show the corresponding transrot plots:

Ulmschneider MB, Sansom MS, and Di Nola A. Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys J 2006 Mar 1; 90(5) 1650-60. doi:10.1529/biophysj.105.065367 pmid:16339877. PubMed HubMed [BJ2006]

Which energies do you use for the plotting (z-axis) ? The generalized born or the complete energy "E" ?
In my case, the simulation produced extreme high values for both energies in compare to your values (e.g. AchR M2 has a range of -4 to 0 on the z-axis).

I'm really sorry for all this rookie questions, but I need this answers to understand this function of hippo and avoid greater problems/failures. I'm really thankful for every help !
Your M.kalavera

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: Transrotscan: How to use it correctly ?

Post by martin » Wed May 06, 2009 11:55 am

Hi,

E-Einf is the total energy minus the total energy at 'infinity', this means a distance z_inf away from the membrane (default is 500 Angstroms), you can set this value in the input file. You can change the grid with dz, dtheta, and dphi. As the conformation is rigid this corresponds to the energy of the peptide-membrane interaction (Egb+Esasa). The phi variable is automatically optimized (this is the rotation around the helix long axis if your peptide is a helix).

The energies you get will depend very strongly on the sequence. If you have highly charged peptides these values can be astronomical due to the large Born terms. This is somewhat unrealistic, in a real membrane water molecules will be dragged into the bilayer or the sidechain might neutralize reducing the energetic penalty. You can neutralize some residues to check the difference. The insertion potential can be adjusted by empirically increasing the membrane surface tension (sigma_membrane). This might be necessary for larger systems.

Good luck and hope this helps!
Martin

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Re: Transrotscan: How to use it correctly ?

Post by m.kalavera » Fri May 08, 2009 7:44 am

Thanks Martin,
this explanation helped allot and made it much more clear to me. As you say, the high charge values of my protein could cause the exorbitant and very unrealistic energies and be very troublesome, I will check the whole system with deprotonated residues. This setups are already running and I will give you an insight about the differences between those two simulations, when I have them.
Thanks again for all your help and kindness,
your M.Kalavera

Post Reply