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Ca-rmsd as a function of frame. Alignment based on 2mer
*[[AD or BC dimers of native HrcQb, T40I-HrcQb, T40Y-HrcQb, T40W-HrcQb]]. Alignments based on the whole . . . of the N-terminus. *[[AB or CD dimers of the HrcQb-like FliN]] . . .
1K - last updated 2004-10-19 14:25 UTC by natasa.biology.uoc.gr
Ca-rmsd as a function of frame. Alignment based on 4mer
*[[native HrcQb, T40I-HrcQb, T40Y-HrcQb, T40W-HrcQb]]. Frames fitting was based on the whole structure . . . 11-14 of the N-terminus (color line). *[[HrcQb-like FliN]]. Frames fitting was based on the . . .
1K - last updated 2004-10-13 14:40 UTC by natasa.biology.uoc.gr
Heating-up NAMD script for HrcQb dimer
<source> # To run this script type: namd2 <filename> # modified # Based on the NAMD-VMD online . . .
3K - last updated 2004-10-12 11:22 UTC by server.cluster.mbg.gr
HrcQb
HrcQb, a low molecular-weight (14 kDa) hydrophilic protein, is a component of the P. syringae Hrp secretion . . . and is encoded by a conserved hrc gene (hrcQb). Based on the similarities of this secretion . . . system with flagellar assemply, HrcQb is assumed to be a structural protein of the . . . cytoplasm as it homologous FliN. The full length HrcQb protein is sensitive to proteolysis and had resisted . . . domain (the last 84 aa, hereafter referred as HrcQb-C) is stable and its structure has been determined . . .
1K - last updated 2004-10-02 15:37 UTC by natasa.biology.uoc.gr
Molecular dynamics studies of HrcQb
This project is in collaboration with IMBB, FORTH. Person responsible : Dr Vasiliki E. Fadouloglou (fadoulog@imbb.forth.gr) . . . the files needed]] * Simulation of native HrcQb **[[heating-up NAMD script]] **[[equilibration . . . **[[equilibration graphs]] * Simulation of HrcQb-like FliN (tetramer) **[[heating-up NAMD script . . . graphs for FliN 4mer]] * Simulation of the AD HrcQb dimer ** [[Heating-up NAMD script for HrcQb dimer]] . . . *Simulation of the BC HrcQb dimer **[[heating-up NAMD script for BC 2mer]] . . .
2K - last updated 2004-10-19 14:04 UTC by natasa.biology.uoc.gr
More on eigenvectors and eigenvalues
Calculation of eigenvalues and eigenvectors is the first step for performing a large number of other . . . (or /vmd/, /pymol/, ...) : [[image: Motion of HrcQb due to principal component]] == Essential dynamics . . .
6K - last updated 2006-02-22 15:12 UTC by server.cluster.mbg.gr
NAMD benchmarks and scaling-up
The tests were performed with a 59428-atom system, identical with the one used for the [[Molecular dynamics . . . studies of HrcQb]]. A short (1000 steps) MD run was performed . . .
2K - last updated 2004-06-29 11:49 UTC by server.cluster.mbg.gr
NAMD benchmarks and scaling-up, enhanced
The previous tests had three problems : * The assumption of an ideal linear scale-up is wrong because . . . (8 nodes) || 67216 || 3.06 || || T40Y mutant of HrcQb-C || PIIIs@733 (9 nodes) || 59696 || 5.10 || . . .
5K - last updated 2004-07-08 14:05 UTC by server.cluster.mbg.gr
Research projects
* [[Molecular dynamics studies of HrcQb]] * [[Parallelisation of a molecular replacement program]] * . . .
1K - last updated 2006-03-23 18:15 UTC by server.cluster.mbg.gr
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