Search found 18 matches

by oliver
Wed Jul 28, 2010 1:01 pm
Forum: Bugs and feature requests
Topic: problem logging into the wiki
Replies: 1
Views: 8635

Re: problem logging into the wiki

Thanks, we're looking into it.
by oliver
Sun Jan 10, 2010 1:52 pm
Forum: Force fields
Topic: lipidbook - force field parameters for membrane simulation
Replies: 0
Views: 12874

lipidbook - force field parameters for membrane simulation

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...
by oliver
Tue Oct 06, 2009 3:09 pm
Forum: Visualization
Topic: Visualization of the membrane
Replies: 4
Views: 12179

Re: Visualization of the membrane

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...
by oliver
Mon Dec 08, 2008 3:26 pm
Forum: Running simulations
Topic: Benchmark page on wiki
Replies: 2
Views: 3023

Conclusion from Benchmark page on wiki

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.
by oliver
Mon Dec 08, 2008 3:22 pm
Forum: Running simulations
Topic: Benchmark page on wiki
Replies: 2
Views: 3023

Re: Benchmark page on wiki

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.
by oliver
Sun Dec 07, 2008 8:59 pm
Forum: Announcements
Topic: Release of Hippo BETA rev 35
Replies: 0
Views: 13313

Release of Hippo BETA rev 35

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

Notes on important changes are summarized in the ChangeLog.
by oliver
Fri Nov 14, 2008 2:53 pm
Forum: Running simulations
Topic: Benchmark page on wiki
Replies: 2
Views: 3023

Benchmark page on wiki

I started a simple Hippo Benchmark page on the wiki.

Basically, just run under Linux

Code: Select all

cd testjobs
time ./calc_testjobs
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.)
by oliver
Tue Nov 11, 2008 5:20 pm
Forum: Announcements
Topic: Release of Hippo BETA Rev. 30
Replies: 0
Views: 7757

Release of Hippo BETA Rev. 30

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...
by oliver
Mon Oct 20, 2008 10:24 pm
Forum: Feature requests
Topic: alternative input file name
Replies: 0
Views: 6553

alternative input file name

Right now the input file must be called hippo_input.txt and hippo automatically reads it:

Code: Select all

hippo
Sometimes it would be quite useful if one could have differently named input files and then use it as

Code: Select all

hippo /path/to/inputfile.txt
.
by oliver
Sat Oct 18, 2008 7:41 pm
Forum: Simulation setup
Topic: Automating setup
Replies: 0
Views: 7381

Automating setup

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...