Wednesday, May 30, 2018

Primitive cluster monitoring for the desktop


Combine warewulf, a tiny cgi perl script and conky, and there it is, a primitive cluster monitoring tool for the desktop without ssh :





Tuesday, May 29, 2018

Renewing cluster hardware


After almost nine years, the hardware from the old norma cluster (circa 2009) is useless for all practical purposes. Have been thinking about the possibility of preserving its (still) functional part and only upgrade the GPUs. Given that the CPUs are weak (Q6600 Kentsfield 2.4 GHz quad processors) I thought I could try with a cheap GPU and see how it goes. Adding a GTX1070 wouldn't make sense, so the first attempt was a GTX1050. The golden standard for comparing the performance is scarlet (i7-6800K@3.4GHz + GTX-1070). The findings were not surprising (system with 9418 atoms and a 4 fs/step using HMR) :
  • Scarlet (i7-6800K @ 3.4GHz + GTX-1070)                 ==>  445 ns/day
  • Old AMD FX-8150, 8 cores @ 3.6 GHz + GTX 1050  ==>  195 ns/day
  • Old Q6600 @ 2.4GHz box + GTX 1050                      ==>  135 ns/day

Given the current price of a GTX1050 (~190 €) would it may make sense to order a handful of 1050s ? An additional test is to replace the boxes altogether with 8 core AMDs. Have ordered a relatively inexpensive box containing an AMD FX 8350 @ 4 GHz + a GTX 1050. The results were : (work in progress)


Saturday, December 23, 2017


Just came out :

«Folding Simulations of a Nuclear Receptor Box-Containing Peptide Demonstrate the Structural Persistence of the LxxLL Motif Even in the Absence of Its Cognate Receptor»




Tuesday, November 28, 2017

Amber 14SB vs 99SB-STAR-ILDN [2]


Have been looking for a mostly disordered peptide (with NMR data available) for which the two force fields would demonstrate detectably different secondary structure preferences. I think I found one :


The upper graph is from 99SB-STAR-ILDN, the lower from 14SB. The two simulations were 24 μs each, both using adaptive tempering (280K-380K). Comparison between observed and calculated  NOEs plus chemical shifts should suffice. Given that this is a mostly disordered peptide ,we should probably also compare the computationally expected vs experimentally observed number of NOEs.



Wednesday, September 27, 2017

Amber 14SB vs 99SB-STAR-ILDN : αLa peptide


Weblogo representations of secondary structure preferences for human α-Lactalbumin 101-111 peptide with the AMBER ff14SB plus a whole lot of other AMBER force fields. The 14SB simulation was 3 μs, all other 2 μs.




On the way from 12SB to 14SB the α-helical preference was significantly reduced, but the mainly 3₁₀-helical nature of this peptide can not be faithfully reproduced. At least for the time, AMBER99SB-STAR-ILDN still looks like the best force field for this peptide.



Friday, September 22, 2017

Amber99SB-STAR-ILDN : tri-alanine


Added one extra diagram to Figure 3 of this paper. This is a 2.6 μs simulation with a 4 fs timestep (HMR). Nearly identical with AMBER 14SB (?).






Sunday, April 23, 2017