Search found 38 matches
- Wed May 06, 2009 11:55 am
- Forum: Analysis
- Topic: Transrotscan: How to use it correctly ?
- Replies: 2
- Views: 10487
Re: Transrotscan: How to use it correctly ?
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...
- Tue May 05, 2009 2:38 pm
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 22948
Re: trouble with MC
In protein folding proteins can get stuck for very long times. In particular if the sequence has a lot of charged sidechains and the temperature is too low. I am seeing similar behaviour at the moment with a peptide that is now at 2 billion MC steps and still not folded propertly. Using a very hydro...
- Tue Apr 21, 2009 8:43 am
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 22948
Re: trouble with MC
Hi, Sorry for the delay! The file looks fine. But your values must start at column number 41, otherwise it will not work. Hippo will print a complete input file with all the parameters you set into log.txt. Please check that it's fine. I think the behavior you see is correct. I'm currently running a...
- Mon Apr 20, 2009 8:58 am
- Forum: Visualization
- Topic: movie.xyz with vmd
- Replies: 2
- Views: 9891
Re: movie.xyz with vmd
Hi, Sorry that's our fault. The hippo xyz file contains all the simulation data (i.e. the entire topology). It cannot currently be viewed with VMD, which just takes coordinates, but we're working on building an add-in for VMD. You can use analyse.exe to convert your xyz into a PDB movie, which you c...
- Thu Apr 16, 2009 9:05 am
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 22948
Re: trouble with MC
Hi,
Sorry you're still having problems.
If you attach your input file, (and maybe the movie.pdb) i'll have a look.
Best wishes,
Martin
Sorry you're still having problems.
If you attach your input file, (and maybe the movie.pdb) i'll have a look.
Best wishes,
Martin
- Wed Apr 15, 2009 12:07 pm
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 22948
Re: trouble with MC
Hi, I just checked and the behavior is indeed correct. The reason for the slower sampling when using GBIM rather than GBSA is that the coulomb interactions are not compensated by solvation forces in the membrane. The membrane part is therefore comparable to a vacuum simulation. In normal GBSA the co...
- Tue Apr 14, 2009 12:36 pm
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 22948
Re: trouble with MC
Hi, It could be that the rigid body moves dominate. These moves were put in to speed up the spatial orientation in the membrane but might be problematic at the start. If you want the protein to stay where it is and not perform any rigid body motion you can set the prob rigidbodymove/MC scan to zero....
- Sun Apr 05, 2009 9:31 am
- Forum: Analysis
- Topic: where is the adiabatic translation+rotation energy scan tool
- Replies: 1
- Views: 8071
Re: where is the adiabatic translation+rotation energy scan tool
Hi,
use mode: transrot scan
you can modify the number of points to scan with: dz, dtheta, dphi
Good luck,
Martin
use mode: transrot scan
you can modify the number of points to scan with: dz, dtheta, dphi
Good luck,
Martin
- Thu Mar 05, 2009 12:54 am
- Forum: Running simulations
- Topic: Simulation crash "Command terminated by signal 6"
- Replies: 2
- Views: 14117
Re: Simulation crash "Command terminated by signal 6"
Hi,
Sorry for the late reply. Can you post or email me your files, i've never seen this kind of error. Sorry for the trouble,
Best wishes
Martin
Sorry for the late reply. Can you post or email me your files, i've never seen this kind of error. Sorry for the trouble,
Best wishes
Martin
- Sun Nov 16, 2008 1:50 pm
- Forum: Running simulations
- Topic: MC steps and MD simulation time
- Replies: 5
- Views: 12788
Re: MC steps and MD simulation time
This sounds very slow. What cutoff are you using? With a 14 Angstrom cutoff you should get at least 1000 moves/s on the Xeon. The MD version of the membrane is implemented and should be much more efficient for larger systems. It still needs a little debugging and probably some form of stochastic dyn...