Search found 6 matches
[phpBB Debug] PHP Warning: in file [ROOT]/vendor/twig/twig/lib/Twig/Extension/Core.php on line 1275: count(): Parameter must be an array or an object that implements Countable- Tue May 12, 2009 6:14 pm
- Forum: Analysis
- Topic: How is the helicity calculated ?
- Replies: 4
- Views: 14530
Re: How is the helicity calculated ?
Hi, Sorry, the helicity analysis is always for the complete simulation, but you can extract the helicity per residue from the helcity_vs_step.dat file, by loading that into e.g. excel and calculating the average of a residue over the time range you need it. The helicity_vs_step.dat file averages eve...
- Tue Apr 21, 2009 1:40 pm
- Forum: Analysis
- Topic: How is the helicity calculated ?
- Replies: 4
- Views: 14530
Re: How is the helicity calculated ?
Hi,
The standard definition of helicity is used. A residue is considered helical if
phi = -57 deg +- 30 deg
psi = -47 deg +- 30 deg
the 'range' is the 30 deg, and can e.g. be narrowed to +- 20 deg. But 30 is recommended. Remember it is +-, so the arc is 60 deg.
Hope this helps,
Jakob
The standard definition of helicity is used. A residue is considered helical if
phi = -57 deg +- 30 deg
psi = -47 deg +- 30 deg
the 'range' is the 30 deg, and can e.g. be narrowed to +- 20 deg. But 30 is recommended. Remember it is +-, so the arc is 60 deg.
Hope this helps,
Jakob
- Tue Oct 14, 2008 5:37 pm
- Forum: Bugs
- Topic: Novice assistance
- Replies: 6
- Views: 39422
Re: Novice assistance
There is a new version of hippo, which also provides executables for older computers
Please get it at www.biowerkzeug.com
enjoy, Jakob
Please get it at www.biowerkzeug.com
enjoy, Jakob
- Wed Oct 08, 2008 9:38 am
- Forum: Bugs
- Topic: Novice assistance
- Replies: 6
- Views: 39422
Re: Novice assistance
Hi, the 'illegal instruction' immediately after starting both on linux and windows looks like a similar 'bug' I wasted a whole day on. hippo is compiled to use SSE2 instruction set for speeding up double precision. Please check your CPU. If it is an Athlon XP you will have problems, because it only ...
- Thu Aug 07, 2008 4:34 pm
- Forum: Force field parameters
- Topic: Improper Dihedrals in HIPPO
- Replies: 1
- Views: 16859
Re: Improper Dihedrals in HIPPO
The dihedrals are treated exactly in the same way as BOSS/MCPRO, including the impropers. Use a V2 torsion only if planarity of geometry is desired, as example, look for e.g. ester torsions, or ring torsions. This approach of course only deals with problems involving theta0 = pi (planarity) There is...
- Thu Aug 07, 2008 3:19 pm
- Forum: Feature requests
- Topic: OpenMP numthreads option with MC simulations
- Replies: 1
- Views: 12444
Re: OpenMP numthreads option with MC simulations
Sorry, MC is not parallelized yet. the openMP numthreads is only for MD simulations. MC will be parallelized in the future.