Search found 6 matches

by jakob
Tue May 12, 2009 6:14 pm
Forum: Analysis
Topic: How is the helicity calculated ?
Replies: 4
Views: 3248

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...
by jakob
Tue Apr 21, 2009 1:40 pm
Forum: Analysis
Topic: How is the helicity calculated ?
Replies: 4
Views: 3248

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
by jakob
Tue Oct 14, 2008 5:37 pm
Forum: Bugs
Topic: Novice assistance
Replies: 6
Views: 10300

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
by jakob
Wed Oct 08, 2008 9:38 am
Forum: Bugs
Topic: Novice assistance
Replies: 6
Views: 10300

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 ...
by jakob
Thu Aug 07, 2008 4:34 pm
Forum: Force field parameters
Topic: Improper Dihedrals in HIPPO
Replies: 1
Views: 3582

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...
by jakob
Thu Aug 07, 2008 3:19 pm
Forum: Feature requests
Topic: OpenMP numthreads option with MC simulations
Replies: 1
Views: 2336

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.