MBG wiki: Search for: NB 40 or 60, swapping threshold 40 or 60

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Block size (constant problem size)
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . parameter values will be used: N : 8000 NB : 40 60 80 100 120 140 160 180 PMAP : Row-major process . . . ||Ax-b||_oo / ( eps * ||A||_1 * ||x||_1 ) = 0.0260008 ...... PASSED ||Ax-b||_oo / ( eps * ||A||_oo . . . T/V N NB P Q Time Gflops ----- WR10R2C4 8000 60 3 3 59.99 5.692e+00 ----- ||Ax-b||_oo / ( eps * . . . N NB P Q Time Gflops ----- WR10R2C4 8000 120 3 3 60.16 5.675e+00 ----- ||Ax-b||_oo / ( eps * ||A||_1 . . .
4K - last updated 2004-06-17 11:48 UTC by server.cluster.mbg.gr

Broadcasts (constant N, NB)
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . N NB P Q Time Gflops ----- WR10R2C4 8000 100 3 3 60.21 5.670e+00 ----- ||Ax-b||_oo / ( eps * ||A||_1 . . . / ( eps * ||A||_oo * ||x||_oo ) = 0.0046096 ...... PASSED ===== T/V N NB P Q Time Gflops ----- . . .
4K - last updated 2004-06-17 11:57 UTC by server.cluster.mbg.gr

Calculation of water and ion distributions
The object of the exercise is to generate a map showing the distribution of waters (hydration pattern) . . . Maximum Centre Range On X : -24.30 24.30 0.00 48.60 On Y : -15.05 15.05 0.00 30.11 On Z : -10.98 15.87 . . . Maximum Centre Range On X : -24.30 24.30 0.00 48.60 On Y : -15.05 15.05 0.00 30.11 On Z : -10.98 15.87 . . .
10K - last updated 2006-01-17 17:18 UTC by server.cluster.mbg.gr

Cluster analysis of trajectories
Read the page [[Calculation of frame-to-frame rmsds]] and then come back. So, now you have your *crossDCD.matrix*. . . . shown below I will assume that your matrix is 460x460 (do a *wc crossDCD.matrix* to determine the . . . > A <- matrix(scan("crossDCD.matrix", n = 460*460), 460, 460, byrow = TRUE) Read 211600 items . . . Distance : euclidean Number of objects: 460 > plclust(hc) > q() Save workspace image? . . . > A <- matrix(scan("crossDCD.matrix", n = 460*460), 460, 460, byrow = TRUE) Read 211600 items . . .
6K - last updated 2005-10-13 11:08 UTC by P.S. Georgoulia

Final HPL 9-node benchmark
In this final test (which was not fully completed due to memory shortage) we tested : * Block size (60, . . . 1 # of problems sizes (N) 15500 Ns 2 # of NBs 60 120 NBs 0 PMAP process mapping (0=Row-,1=Column-major) . . . T/V N NB P Q Time Gflops ----- WR00L2L4 15500 60 3 3 262.50 9.459e+00 WR00L3L4 15500 60 3 3 259.67 . . . 9.562e+00 WR00L2L8 15500 60 3 3 258.72 9.597e+00 WR00L3L8 15500 60 3 3 367.93 . . . 6.748e+00 WR00L2C4 15500 60 3 3 393.35 6.312e+00 WR00L3C4 15500 60 3 3 390.77 . . .
28K - last updated 2004-06-29 11:31 UTC by server.cluster.mbg.gr

Final test with respect to problem size
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . 14000 13000 12000 11000 10000 9000 8000 7000 6000 5000 4000 3000 2000 1000 NB : 60 PMAP : Row-major . . . BCAST : BlongM DEPTH : 0 SWAP : Mix (threshold = 60) L1 : transposed form U : transposed form EQUIL . . . T/V N NB P Q Time Gflops ----- WR05R2C8 15000 60 3 3 235.11 9.571e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR05R2C8 14000 60 3 3 207.70 8.809e+00 ----- ||Ax-b||_oo / ( eps * . . .
6K - last updated 2004-06-25 21:22 UTC by ppp3-51.the.forthnet.gr

HPL benchmarks (8 nodes)
Using the parameters obtained from the 9-node tests, and only testing the grid size the following [[initial . . . 11776 12288 12800 13312 13824 14336 NB : 40 50 60 80 120 PMAP : Row-major process mapping P : 4 2 . . . Blong BlongM DEPTH : 0 SWAP : Mix (threshold = 60) L1 : transposed form U : transposed form EQUIL . . . 2 99.09 7.226e+00 WR01R2C8 10240 50 4 2 98.61 7.260e+00 WR02R2C8 10240 50 4 2 98.45 7.273e+00 WR03R2C8 . . . 10240 50 4 2 98.38 7.278e+00 WR00R2C8 10240 60 4 2 104.58 6.846e+00 WR01R2C8 10240 60 4 2 103.87 . . .
14K - last updated 2004-06-18 06:59 UTC by server.cluster.mbg.gr

HPL benchmarks (9 nodes)
The 9 nodes are the server (Pentium IV) and the 8 newest nodes (Celerons). The mpich library and executables . . . block size with constant BCAST]] : NB=40 or 60 ? * [[NB 40 or 60, swapping threshold 40 or 60]], . . . Ok stick to NB=60, swapping threshold 60. * [[NBmin]] 8 looks better . . .
1K - last updated 2004-07-08 14:08 UTC by server.cluster.mbg.gr

Heating-up NAMD script for HrcQb dimer
<source> # To run this script type: namd2 <filename> # modified # Based on the NAMD-VMD online . . . # heat with CAs restrained # langevin on run 6000 output output/heat_ca # equilibrate volume with . . .
3K - last updated 2004-10-12 11:22 UTC by server.cluster.mbg.gr

Look-ahead depth
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . parameter values will be used: N : 12000 NB : 60 PMAP : Row-major process mapping P : 3 Q : 3 PFACT . . . : BlongM DEPTH : 0 1 SWAP : Mix (threshold = 60) L1 : transposed form U : transposed form EQUIL . . . T/V N NB P Q Time Gflops ----- WR05R2C8 12000 60 3 3 139.04 8.287e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR15R2C8 12000 60 3 3 139.67 8.250e+00 ----- ||Ax-b||_oo / ( eps * . . .
2K - last updated 2004-06-17 13:49 UTC by server.cluster.mbg.gr

NAMD Ala2Ile2 equilibration script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel . . . 80 # <===== CHANGE ME PmeGridsizeY 60 # <===== CHANGE ME PmeGridsizeZ 60 # <===== . . . Check me useGroupPressure yes firsttimestep 146000 # <===== CHANGE ME run 5000000 ;# <===== . . .
2K - last updated 2004-11-16 16:21 UTC by server.cluster.mbg.gr

NAMD Ala2Ile2 minimization and heating-up script
<source> # # Input files # structure ionized.psf coordinates ionized.pdb parameters par_all27_prot_na.inp . . . 80 # <===== CHANGE ME PmeGridsizeY 60 # <===== CHANGE ME PmeGridsizeZ 60 # <===== . . .
3K - last updated 2004-11-16 16:20 UTC by server.cluster.mbg.gr

NAMD Ala2Ile2 restart script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor bincoordinates restart.coor . . . 80 # <===== CHANGE ME PmeGridsizeY 60 # <===== CHANGE ME PmeGridsizeZ 60 # <===== . . . Check me useGroupPressure yes firsttimestep 756000 # <===== CHANGE ME run 4390000 ;# <===== . . .
2K - last updated 2004-11-16 16:24 UTC by papaioannou

NAMD benchmarks and scaling-up
The tests were performed with a 59428-atom system, identical with the one used for the [[Molecular dynamics . . . || || 4 || 4.755 || 3.67 || || 6 || 3.799 || 4.60 || || 8 || 2.794 || 6.25 || || 9 || 2.616 || 6.67 . . . || || 4 || 4.755 || 3.67 || || 6 || 3.799 || 4.60 || || 8 || 2.794 || 6.25 || || 9 || 2.616 || 6.67 . . .
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 . . . || 5.7692 || 0.730 || 12.72 || || 9 || 2.5607 || 4.59718 || 6.4505 || 0.712 || 13.88 || || 10 . . . || 14.50 || || 14 || 2.2582 || 5.21300 || 8.1060 || 0.643 || 15.74 || || 15 || 2.1695 || 5.42613 . . . two independent jobs is the following : For a 60000-atom system using all nodes simultaneously would . . .
5K - last updated 2004-07-08 14:05 UTC by server.cluster.mbg.gr

NAMD equilibration script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel . . . 64 # <===== CHANGE ME PmeGridsizeZ 60 # <===== CHANGE ME # # Periodic boundary things . . . Check me useGroupPressure yes firsttimestep 146000 # <===== CHANGE ME run 5000000 ;# <===== . . .
2K - last updated 2004-11-16 16:16 UTC by georgoulia

NAMD minimisation and heating-up script
<source> # # Input files # structure ionized.psf coordinates ionized.pdb parameters par_all27_prot_na.inp . . . 64 # <===== CHANGE ME PmeGridsizeZ 60 # <===== CHANGE ME # # Periodic boundary things . . . # <===== CHANGE ME cellBasisVector2 00.00 60.14 00.00 # <===== CHANGE ME cellBasisVector3 . . .
3K - last updated 2004-11-12 11:17 UTC by server.cluster.mbg.gr

NAMD minimization and heating-up script
<source> # # Input files # structure ionized.psf coordinates ionized.pdb parameters par_all27_prot_na.inp . . . 80 # <===== CHANGE ME PmeGridsizeY 60 # <===== CHANGE ME PmeGridsizeZ 60 # <===== . . .
3K - last updated 2004-11-16 16:07 UTC by server.cluster.mbg.gr

NAMD restart2 script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor bincoordinates restart2.coor . . . 64 # <===== CHANGE ME PmeGridsizeZ 60 # <===== CHANGE ME # # Periodic boundary things . . .
2K - last updated 2004-11-16 16:24 UTC by georgoulia

NAMD restart script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor bincoordinates restart.coor . . . 64 # <===== CHANGE ME PmeGridsizeZ 60 # <===== CHANGE ME # # Periodic boundary things . . .
2K - last updated 2004-11-16 16:22 UTC by georgoulia

NAS Parallel Benchmarks, v.2.3, 4 old nodes
The benchmarks were built with the Intel compilers. MPICH was used as the MPI implementation. Process . . . Time step 1 Time step 20 Time step 40 Time step 60 Time step 80 Time step 100 Time step 120 Time step . . . 140 Time step 160 Time step 180 Time step 200 Verification being performed . . . 5 0.2527896321175E+03 0.2527896321175E+03 0.1394160013545E-13 Comparison of RMS-norms of solution error . . . 1 0.4234841604053E+01 0.4234841604053E+01 0.1468118413674E-14 . . .
9K - last updated 2004-07-01 10:47 UTC by server.cluster.mbg.gr

NAS Parallel Benchmarks, v.2.3, 4 old nodes, Class B
Same thing but with some class B problems : == NAS Parallel Benchmarks 2.3 -- BT Benchmark == No input . . . Time step 1 Time step 20 Time step 40 Time step 60 Time step 80 Time step 100 Time step 120 Time step . . . 140 Time step 160 Time step 180 Time step 200 Verification being performed . . . 0.9933052259015E+02 0.9933052259015E+02 0.3576658600156E-14 3 0.3564602564454E+03 0.3564602564454E+03 . . . 0.4463289611567E+01 0.4463289611567E+01 0.1313376025349E-13 3 0.1312257334221E+02 0.1312257334221E+02 . . .
6K - last updated 2004-07-01 12:24 UTC by server.cluster.mbg.gr

NB 40 or 60, swapping threshold 40 or 60
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . parameter values will be used: N : 10000 NB : 60 PMAP : Row-major process mapping P : 3 Q : 3 PFACT . . . BCAST : BlongM DEPTH : 1 SWAP : Mix (threshold = 60) L1 : transposed form U : transposed form EQUIL . . . T/V N NB P Q Time Gflops ----- WR15R2C4 10000 60 3 3 91.87 7.259e+00 ----- ||Ax-b||_oo / ( eps * . . .
4K - last updated 2004-06-17 13:17 UTC by server.cluster.mbg.gr

NBmin
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . parameter values will be used: N : 12000 NB : 60 PMAP : Row-major process mapping P : 3 Q : 3 PFACT . . . BCAST : BlongM DEPTH : 1 SWAP : Mix (threshold = 60) L1 : transposed form U : transposed form EQUIL . . . T/V N NB P Q Time Gflops ----- WR15R2C4 12000 60 3 3 139.85 8.239e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR15R2C8 12000 60 3 3 138.86 8.297e+00 ----- ||Ax-b||_oo / ( eps * . . .
2K - last updated 2004-06-17 13:42 UTC by server.cluster.mbg.gr

Qs tests on MBG cluster
The version of Qs used is dated September, 10th, 2004. The parallel version was compiled with mpicc . . . 752 || 1.404 || || 4156 || P222 || 4 || 659 || 1.602 || || 4156 || P222 || 6 || 661 || 1.597 || || 4156 . . .
5K - last updated 2004-10-02 14:37 UTC by server.cluster.mbg.gr

Real Programmers Don't Write Pascal
In the good old days - the "Golden Era" of computers, it was easy to separate the real men from the . . . toggles the first operating system for the CDC-7600 in on the front panel from memory when it was first . . .
22K - last updated 2004-10-10 20:45 UTC by ppp1-68.axd.forthnet.gr

Running NAMD on the cluster via SGE
There are two ways to run NAMD on the cluster : the old way, and the new way. = The old way = Is to . . . remaining, 13975 kB of memory in use. TIMING: 600 CPU: 512.58, 0.83405/step Wall: 520.755, 0.847025/step, . . . 0.83345/step Wall: 866.847, 0.849677/step, 0.236021 hours remaining, 15687 kB of memory in use. TIMING: . . . remaining, 15687 kB of memory in use. TIMING: 1600 CPU: 1347.06, 0.8353/step Wall: 1377.96, 0.849509/step, . . . remaining, 13973 kB of memory in use. TIMING: 600 CPU: 512.48, 0.83485/step Wall: 525.369, 0.85418/step, . . .
5K - last updated 2005-06-30 07:19 UTC by glykos

Running a molecular dynamics simulation of a tetrapeptide in a truncated octahedral cell
----- ----- Go read & do the previous tutorials on Rop and protein G, then come back ... (read also . . . Check me useGroupPressure yes firsttimestep 9600 # <===== CHANGE ME run 5000000 ;# <===== . . .
7K - last updated 2005-10-28 16:57 UTC by server.cluster.mbg.gr

Running a molecular dynamics simulation of native Rop
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . C ATOM 4 O MET A 1 32.375 0.280 16.846 1.00 23.60 O ..... ATOM 445 CE1 PHE A 56 38.342 8.335 16.790 . . . C ATOM 4 O MET B 1 73.312 0.280 36.526 1.00 23.60 O ..... ATOM 446 CE2 PHE B 56 66.157 7.284 34.719 . . . 1.00 23.77 C ATOM 447 CZ PHE B 56 66.160 7.962 35.952 1.00 24.84 C TER 448 PHE B 56 END . . . Maximum Centre Range On X : -39.30 39.30 0.00 78.60 On Y : -30.05 30.05 0.00 60.10 On Z : -25.98 30.85 . . .
27K - last updated 2005-09-27 12:03 UTC by server.cluster.mbg.gr

Running a molecular dynamics simulation of protein G in a hexagonal cell
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . LOAD BALANCE STRATEGY Other Info: LDB PERIOD 1600 steps Info: FIRST LDB TIMESTEP 40 Info: LDB BACKGROUND . . . in use. Info: Entering startup phase 2 with 3960 kB of memory in use. Info: Entering startup phase . . . (700) Info: Entering startup phase 8 with 6088 kB of memory in use. Info: Finished startup with . . . -21040.4570 363518.9081 0.0000 0.0000 0.0000 345608.0905 0.0000 345608.0905 345608.0905 0.0000 1220671.1003 . . .
25K - last updated 2005-09-27 12:05 UTC by server.cluster.mbg.gr

Running a molecular dynamics simulation of the Dickerson (DNA) dodecamer
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . 24.100 1.00 31.28 1BNA 69 ATOM 8 O4* C A 1 19.360 31.583 24.852 1.00 37.45 1BNA 70 ...... ATOM 493 . . . On Y : -29.96 30.01 0.03 59.97 On Z : -30.39 29.60 -0.39 60.00 ** Note these numbers, especially the . . . 80 # <===== CHANGE ME PmeGridsizeY 60 # <===== CHANGE ME PmeGridsizeZ 60 # <===== . . . # <===== CHANGE ME cellBasisVector2 00.00 60.00 00.00 # <===== CHANGE ME cellBasisVector3 . . .
30K - last updated 2005-09-27 12:04 UTC by server.cluster.mbg.gr

Secondary structure analysis of protein trajectories
/vmd/ plus a few tricks : * Create in your current directory (assumed to contain your protein-only trajectory . . . #include <ctype.h> #define HCOL 160,32,240 /* Alpha helix */ #define GCOL 203,78,97 . . .
8K - last updated 2005-06-30 13:41 UTC by glykos

Software updates, known 'features', etc.
== April 11th, 2006 == * molmol v.2K-2 installed clusterwide. == March 20th, 2006 == * Haploview and . . . The line reading IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 should read IC CD1 . . . CD2 *CG HG 1.5361 110.2600 116.6300 108.0200 1.1168 The result is that the . . .
2K - last updated 2006-04-11 14:20 UTC by server.cluster.mbg.gr

Why I write C
I would like to find the proper credit for the material below. Please mail me if you know the author. . . . system, that it only just ran on those Sun 3/60 things. They had all the ingredients for what I . . .
12K - last updated 2004-09-28 15:47 UTC by server.cluster.mbg.gr

gcc 2.95.3, atlas 3.6.0 local compilation
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . N : 8000 9000 10000 11000 12000 13000 14000 NB : 60 PMAP : Row-major process mapping P : 3 Q : 3 PFACT . . . T/V N NB P Q Time Gflops ----- WR10R2C4 8000 60 3 3 60.77 5.618e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR10R2C4 9000 60 3 3 78.58 6.186e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR10R2C4 10000 60 3 3 97.99 6.805e+00 ----- ||Ax-b||_oo / ( eps * . . .
4K - last updated 2004-06-17 11:19 UTC by server.cluster.mbg.gr

heating-up NAMD script
<source> # To run this script type: namd2 <filename> # modified # Based on the NAMD-VMD online . . . # heat with CAs restrained # langevin on run 6000 output output/heat_ca # equilibrate volume with . . .
3K - last updated 2004-10-12 11:16 UTC by server.cluster.mbg.gr

heating-up NAMD script for T40I
<source> # To run this script type: namd2 <filename> # modified # Based on the NAMD-VMD online . . . # heat with CAs restrained # langevin on run 16000 output output/heat_ca # equilibrate volume with . . .
3K - last updated 2004-10-19 14:28 UTC by natasa.biology.uoc.gr

heating-up NAMD script for T40W
<source> # To run this script type: namd2 <filename> # modified # Based on the NAMD-VMD online . . . # heat with CAs restrained # langevin on run 6000 output output/heat_ca # equilibrate volume with . . .
3K - last updated 2004-10-12 11:23 UTC by server.cluster.mbg.gr

heating-up NAMD script for T40Y
<source> # To run this script type: namd2 <filename> # modified # Based on the NAMD-VMD online . . . # heat with CAs restrained # langevin on run 6000 output output/heat_ca # equilibrate volume with . . .
3K - last updated 2004-10-12 11:22 UTC by server.cluster.mbg.gr

icc, mpich, gcc-made cblas
Compiler : icc -xK -tpp6 -O3 -static -O3 -unroll -ip Libraries : atlas, cblas (gcc-made) MPI : mpich . . . be used: N : 8000 9000 10000 11000 12000 NB : 60 PMAP : Row-major process mapping P : 3 Q : 3 PFACT . . . T/V N NB P Q Time Gflops ----- WR10R2C4 8000 60 3 3 71.60 4.769e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR10R2C4 9000 60 3 3 97.22 5.000e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR10R2C4 10000 60 3 3 124.84 5.341e+00 ----- ||Ax-b||_oo / ( eps * . . .
3K - last updated 2004-06-16 08:50 UTC by server.cluster.mbg.gr

icc, mpich, intel math kernel library
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . N : 8000 9000 10000 11000 12000 13000 14000 NB : 60 PMAP : Row-major process mapping P : 3 Q : 3 PFACT . . . T/V N NB P Q Time Gflops ----- WR10R2C4 8000 60 3 3 69.59 4.907e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR10R2C4 9000 60 3 3 93.32 5.209e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR10R2C4 10000 60 3 3 121.69 5.480e+00 ----- ||Ax-b||_oo / ( eps * . . .
3K - last updated 2004-06-17 10:25 UTC by server.cluster.mbg.gr

initial 8-node HPL results
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . parameter values will be used: N : 14336 NB : 60 PMAP : Row-major process mapping P : 4 2 Q : 2 4 . . . BCAST : BlongM DEPTH : 0 SWAP : Mix (threshold = 60) L1 : transposed form U : transposed form EQUIL . . . T/V N NB P Q Time Gflops ----- WR05R2C8 14336 60 4 2 213.22 9.214e+00 ----- ||Ax-b||_oo / ( eps * . . . T/V N NB P Q Time Gflops ----- WR05R2C8 14336 60 2 4 257.40 7.632e+00 ----- ||Ax-b||_oo / ( eps * . . .
2K - last updated 2004-06-17 16:44 UTC by server.cluster.mbg.gr

re-refine block size with constant BCAST
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . will be used: N : 8000 NB : 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 PMAP : Row-major . . . / ( eps * ||A||_oo * ||x||_oo ) = 0.0046600 ...... PASSED ===== T/V N NB P Q Time Gflops ----- . . . T/V N NB P Q Time Gflops ----- WR15R2C4 8000 60 3 3 56.22 6.073e+00 ----- ||Ax-b||_oo / ( eps * . . . / ( eps * ||A||_oo * ||x||_oo ) = 0.0043607 ...... PASSED . . .
4K - last updated 2004-06-17 13:10 UTC by server.cluster.mbg.gr

χ-value analysis (including χ1-χ2 plots and residence times)
In order to examine what rotamers a particular residue occupies during the trajectory, you need to calculate . . . if the values of the angles are between 0 and 360 degrees. Probably /xplor/ will give values from . . . "%15.6f %15.6f\n", val1, val2); else { val2+=360.0; printf( "%15.6f %15.6f\n", val1, val2); } } } . . .
5K - last updated 2005-06-30 13:39 UTC by glykos

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