biowerkzeug

Thanks, we're looking into it.

A shameless plug for a new website that we developed: lipidbook.bioch.ox.ac.uk is a repository for force field parameters that are used in simulations of membranes and membrane proteins. You can download parameter sets find the paper in which the parameters were published comment on parameter sets u...

The definition of the membrane from gbsw.doc : 4. Low-dielectric slab for membrane The influence of membrane hydrophobic core as the low dielectric medium is approximately captured in the GBSW module (see reference 2 for details). Note that the membrane switching function is applied in the following...

Tentative conclusions:

• It does not matter if you use the hippo or hippo_p3 binary (at least for the revisions tested).
• The MD code only scales up to ~4 cores (with a factor of about 3.3) (tested on the WALP+octane MD test case).
• Fast Intel processors are good.

I added scaling benchmarks to the wiki page.

I simply ran the WALP + octane MD simulation, took the time and plotted the results. The general results (for this system) appear to be that performance gains beyond 4 cores are negligible.

Find the latest release (r35) at the download page http://www.biowerkzeug.com/ .

Notes on important changes are summarized in the ChangeLog.

I started a simple Hippo Benchmark page on the wiki.

Basically, just run under Linux and report the user time and the cpu.

(Completely un-scientific but probably better than nothing and gives a first indication of relative performance of architectures.)

Please download the latest version Hippo BETA Rev. 30 from www.biowerkzeug.com . Separate downloads are available for Windows and Linux. This release features the new dynamic input file loader (which should relax the stringent requirement on the input file format of previous versions). For more deta...

Right now the input file must be called hippo_input.txt and hippo automatically reads it: Sometimes it would be quite useful if one could have differently named input files and then use it as .

When using hippo one typically sets up a working directory WORK_DIR, copies input files and the executable to the directory and then executes hippo from within WORK_DIR. I got tired of doing this manually so I wrote a bash script for Linux hippo_setup.sh which automates the setup/copying task. Basic...