biowerkzeug

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 ...

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

There is a new version of hippo, which also provides executables for older computers

Please get it at www.biowerkzeug.com

enjoy, Jakob

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 ...

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 ...

Sorry, MC is not parallelized yet. the openMP numthreads is only for MD simulations. MC will be parallelized in the future.