Search found 10 matches

by kaihsu
Wed Jul 28, 2010 10:06 am
Forum: Bugs and feature requests
Topic: problem logging into the wiki
Replies: 1
Views: 4595

problem logging into the wiki

I tried to log into the wiki but got this error: Warning: is_dir() [function.is-dir]: open_basedir restriction in effect. File(../subdomains/forums/httpdocs) is not within the allowed path(s): (/var/www/vhosts/biowerkzeug.org/httpdocs:/tmp) in /var/www/vhosts/biowerkzeug.org/httpdocs/extensions/Auth...
by kaihsu
Mon Nov 17, 2008 4:42 pm
Forum: Running simulations
Topic: MC steps and MD simulation time
Replies: 5
Views: 2794

Re: MC steps and MD simulation time

Thanks! I changed the cutoff from 44 Å to 14 Å and am getting about 200 moves per second.
by kaihsu
Fri Nov 14, 2008 11:32 am
Forum: Feature requests
Topic: MD simulations
Replies: 2
Views: 2987

Re: MD simulations

Thanks to the Ulmschneider brothers for the tool Hippo. As I said elsewhere: ‘I wonder whether it is possible to implement parallel MD with implicit membranes, and how fast would that be?’ viewtopic.php?f=13&t=18
by kaihsu
Fri Nov 14, 2008 11:28 am
Forum: Running simulations
Topic: MC steps and MD simulation time
Replies: 5
Views: 2794

benchmarking (Re: MC steps and MD simulation time)

I have a system of 10400 atoms (1293 residues). I am running Monte Carlo (MC) with implicit membrane with hippo [with Supplemental Streaming SIMD Extension 3 (SSSE3)]. For this, a scan is about 1e4 moves; let’s say this corresponds to a 2 fs molecular dynamics (MD) time-step. The fastest I can get o...
by kaihsu
Thu Nov 13, 2008 4:13 pm
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 11107

Re: rattle: too many constraint iterations.

Ah of course! I should have used ‘mode MC simulation’ rather than ‘mode MD simulation’. After this change, it works. (Thanks to Martin for the tip.)
by kaihsu
Thu Nov 13, 2008 3:46 pm
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 11107

rattle: too many constraint iterations.

I got this error when running a Monte Carlo simulation with implicit solvent and membranes: rattle: too many constraint iterations. Then Hippo quits. What should I check? Is it because the protein is too large, or there are too many clashes, or something more insiduous? Input file: hippo input file ...
by kaihsu
Thu Nov 13, 2008 11:53 am
Forum: Force field parameters
Topic: spermine?
Replies: 2
Views: 5907

Re: spermine?

Thanks! I will check.
by kaihsu
Wed Nov 12, 2008 3:50 pm
Forum: Force field parameters
Topic: spermine?
Replies: 2
Views: 5907

spermine?

What would the entry for spermine look like in hippo_protein_database.dat? I have the following ligand and would like to perform a simulation with Hippo: HETATM10361 N1 SPM E 1 -0.020 1.240 61.830 1.00 0.00 N HETATM10362 HAA SPM E 1 -0.090 0.710 62.670 1.00 0.00 H HETATM10363 HAB SPM E 1 0.850 1.740...
by kaihsu
Wed Nov 12, 2008 3:33 pm
Forum: White Noise
Topic: Biowerkzeug European Cooperative Society?
Replies: 0
Views: 8896

Biowerkzeug European Cooperative Society?

Maybe Biowerkzeug should incorporate as a European Cooperative Society?
http://en.wikipedia.org/wiki/European_C ... ve_Society