![[Home]](/wiki.png)
2008-01-09
- Eisagogi tou vivliou 'Genome' by Matt Ridley gia tis ergasies sti Genetiki Anthropou. - Also, ena timetable . . .
1K - last updated 2008-01-09 11:11 UTC by server.cluster.mbg.gr
2008-05-16
ebala biotexnologia 2 nees dialekseis kai lab notes (apo internet)g etos 2008 . . .
1K - last updated 2008-10-13 13:17 UTC by server.cluster.mbg.gr
A linux virus ...
See http://math-www.uni-paderborn.de/~axel/bliss/ for the whole story ... Subject: Re: [masq] 1st virus . . . called Bliss > which infects Linux executables. > Its target is users who play games such . . . binaries when it runs. McAfee's statements about this are, at best, misleading. To quote from . . . have discovered the first computer virus capable of infecting the Linux operating system. Whatever . . . there was a CERT several years ago about IRC, for example. The virus, which is called . . .
4K - last updated 2005-09-19 15:18 UTC by server.cluster.mbg.gr
Accuracy and stability issues
There are some accuracy and stability issues concerning the molecular dynamics methods described in the . . . integration scheme hovers at the limit of instability. The practical experience, at least with proteins . . . all)). This has been shown in the past to be stable up-to and including a Δt=8fs, see the paper by . . . For DNA simulations though, it is probably better to follow Marc's advice. == Message 1== . . . Constraint failure; simulation has become unstable. ERROR: Exiting prematurely. ===== WallClock: . . .
7K - last updated 2005-06-30 12:35 UTC by glykos
Backing-up molecular dynamics simulation data
As yet there is no DVD writter available, so you will have to use CDs. Plenty of CDs. The basic idea . . .
7K - last updated 2005-06-23 09:07 UTC by glykos
Backup, backup, backup ...
# What's the point of doing a simulation if you are going to loose all the data (and their analyses) . . . a hard disk failure ? _None_ # What is the probability of a hard disk failure given enough time ? . . . 1.0 # What is the probability according to Murphy's law that the 'enough . . . time' above will coincide with the day that your simulation . . . and analyses finish ? 1.0 Points 1, 2 and 3 above imply that == Data loss due to missing backups . . .
2K - last updated 2005-06-08 14:49 UTC by glykos
Benchmarking and scale-up
For trivially parallel problems (running, for example, many independent instances of the same program . . . To get a feeling for this number, the following table shows what position in the top 500 fastest supercomputers . . .
2K - last updated 2009-02-17 20:18 UTC by ppp1-31.axd.forthnet.gr
Block size (constant problem size)
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
4K - last updated 2004-06-17 11:57 UTC by server.cluster.mbg.gr
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 . . . excluding residues 11-14 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
Calculation of water and ion distributions
The object of the exercise is to generate a map showing the distribution of waters (hydration pattern) . . . with the practical issues, you should be warned about the two most notable shortcomings of the suggested . . . the density map will be build). You should probably use the second method. == Method 1 (creates large . . . an existing DCD using /catdcd/. You should probably avoid including the frames corresponding to the . . . will be calculated. If you did what suggested above (and the first frame of your DCD is the first . . .
10K - last updated 2006-01-17 17:18 UTC by server.cluster.mbg.gr
Cationic peptide simulation (ph 2)
The difficulty is building a protonated (COOH) C-terminal group. The solution is simple: use a modified . . . both of which should be available from within /usr/local/charmm27/ . . .
1K - last updated 2006-02-02 15:33 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*. . . . 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute . . . 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' . . . 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute . . . 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' . . .
6K - last updated 2005-10-13 11:08 UTC by P.S. Georgoulia
Comparison of sets of eigenvectors
If you have two independent trajectories (or, two independent pieces from the same trajectory), you may . . . The C program that follows implements the above equation. It will read a specified number of . . . k2 ) { printf("Dimensions of vectors not equal. Abort.\n"); exit( 1 ); } /* The actual calculation . . .
5K - last updated 2007-03-06 14:34 UTC by server.cluster.mbg.gr
Create the files needed
*What is needed: **A force field parameter file **A force field topology file **A pdb file with the initial . . . file predicts coordinates for atoms which are absent from the start-H2O.pdb i.e. flexible atoms of . . .
2K - last updated 2004-10-11 09:26 UTC by server.cluster.mbg.gr
Eigenvectors and eigenvalues, sufficient sampling issues
Doing a principal component analysis (PCA) of a trajectory is easy. And is even easier to prepare nice . . . and simple. Being careful is this : you must be able to demonstrate that you have sufficiently sampled . . . your molecule has two major and relatively stable conformers, you may have sufficient sampling of . . . seen in your dynamics). In this case you may be able to demonstrate sufficient sampling for these conformers . . .
5K - last updated 2005-10-17 10:59 UTC by server.cluster.mbg.gr
Electrostatics calculations with APBS and PyMol
[[APBS]] is available on all machines *but* PyMol is only available on the newer nodes. You better sit . . . by typping /usr/local/bin/psize.py in the box labeled as such. * Click 'Set grid' at the bottom of . . .
2K - last updated 2005-12-03 15:19 UTC by server.cluster.mbg.gr
Final HPL 9-node benchmark
In this final test (which was not fully completed due to memory shortage) we tested : * Block size (60, . . . benchmark input file Innovative Computing Laboratory, University of Tennessee HPL.out output file . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
6K - last updated 2004-06-25 21:22 UTC by ppp3-51.the.forthnet.gr
Force field
All simulations run under CHARMM force field using the NAMD program. The conditions for all simulations . . . are: constant number of particles (N), stable pressure (P= 1.01325 bars = 1 atm), stable temperature . . .
1K - last updated 2004-10-02 09:45 UTC by server.cluster.mbg.gr
Great Hackers
Great Hackers July 2004 /(This essay is derived from a keynote talk at Oscon 2004.)/ A few months ago . . . alarming book. *Edisons* There's no controversy about which idea is most controversial: the suggestion . . . has no variation in productivity, it's probably not because everyone is Thomas Edison. It's probably . . . That's not a new idea. Fred Brooks wrote about it in 1974, and the study he quoted was published . . . the variation between programmers. He wrote about productivity in lines of code: the best programmers . . .
29K - last updated 2005-05-30 15:25 UTC by glykos
HPL benchmarks (8 nodes)
Using the parameters obtained from the 9-node tests, and only testing the grid size the following [[initial . . . was 9.2 Gflops. A more exhaustive test with variable NB, BCAST, problem size (shown below), indicated . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
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 . . . the celeron nodes (aspera), and it looks reasonably good (reaching 8.2 Gflops). Optimisation : * [[Block . . .
1K - last updated 2004-07-08 14:08 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 . . . last 84 aa, hereafter referred as HrcQb-C) is stable and its structure has been determined by X-ray . . .
1K - last updated 2004-10-02 15:37 UTC by natasa.biology.uoc.gr
Look-ahead depth
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
2K - last updated 2004-06-17 13:49 UTC by server.cluster.mbg.gr
Maintenance
== September 2008 == * PC2 & PC8 dead for good. == March 2008 == * PC2 still missing in action. * . . . * Actually, the air conditioning unit wasn't stable. Cluster room became a water park. Switch everything . . . escaped (?). * Afternoon of June 7th: looking stable ? * Server says "broken RAID". One of the disks . . . digital), rebuilt array, make the new disk bootable (everything from BIOS) : looking good. ** Boot . . . went down again (upon a simple grep). Will probably start worrying soon. == May 10th, 2006 == * Power . . .
9K - last updated 2008-10-13 13:19 UTC by server.cluster.mbg.gr
Molecular dynamics studies of HrcQb
This project is in collaboration with IMBB, FORTH. Person responsible : Dr Vasiliki E. Fadouloglou (fadoulog@imbb.forth.gr) . . .
2K - last updated 2004-10-19 14:04 UTC by natasa.biology.uoc.gr
Molecular dynamics tutorials
* Molecular dynamics tutorials (NAMD-based) : ** [[Running a molecular dynamics simulation of native . . . truncated octahedral cell]] ** [[Accuracy and stability issues]] * [[Cationic peptide simulation (ph . . .
1K - last updated 2006-09-15 14:05 UTC by server.cluster.mbg.gr
More on eigenvectors and eigenvalues
Calculation of eigenvalues and eigenvectors is the first step for performing a large number of other . . . : For these analyses to be valid, you have to be able to show that your simulation sufficiently sampled . . . given frames (ie structures). Large numbers (in absolute value) imply that the corresponding eigenvector . . . the corresponding structure. The unix shell line above determines the range of amplitudes observed in . . . to the corners of the distribution shown above can be highly distorted. == Determination of . . .
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 . . . the slower nodes as well gives the following table : ||Number of processors||Days per nanosecond . . .
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 . . . that the server and celerons would have comparable performance. But, they don't : running NAMD stand-alone . . . faster than the server alone. This is not achievable for two reasons (i) communication overhead, (ii) . . . == The clear conclusion from the analysis above is that the most effective usage of the cluster . . . with the one used for the results shown in the tables above, it is easy to calculate just how well . . .
5K - last updated 2004-07-08 14:05 UTC by server.cluster.mbg.gr
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 . . . Internet: npb@nas.nasa.gov If email is not available, send this to: MS T27A-1 NASA Ames Research Center . . .
9K - last updated 2004-07-01 10:47 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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
2K - last updated 2004-06-17 13:42 UTC by server.cluster.mbg.gr
Network performance (NetPipe results)
All measurements performed with NetPIPE[http://www.scl.ameslab.gov/netpipe/] v.3.6. * [[Raw TCP performance]] . . .
1K - last updated 2004-06-23 13:27 UTC by server.cluster.mbg.gr
OOM killer enabled
We have had some problems with nodes dying under OOM (out-of-memory) conditions (nicelly reproduced by . . . So, it seems that under oM the OOM killer is disabled, which perfectly explains the crashes. A new . . .
2K - last updated 2005-02-05 15:02 UTC by NMG
Performing a molecular dynamics simulation in a truncated octahedral cell
A truncated octahedron is one of the most effective choices for approximately spherical molecules. The . . . in the /vmd/ script. For the example shown above you would have to specify cellBasisVector1 32.00 . . . unit cell dimensions are equal). ----- NOTE about pressure : When /vmd/'s solvate script prepares . . . when the barostat is turned on. You can probably avoid this by specifying in the /vmd/ script a . . .
3K - last updated 2005-09-29 09:26 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 . . . : === For high symmetry space groups it is probably worth using the parallel version. For orthorhombic . . .
5K - last updated 2004-10-02 14:37 UTC by server.cluster.mbg.gr
Quick view of large trajectory (DCD) files
/Carma/ is evolving really fast these days. The rest of this page is history (and as such, is being kept). . . . With the limited physical memory resources available on our nodes (256 MBytes for newer nodes) if you . . . /y/, and /z/), the only representation available is simple dots, and the choice of colours is obscure. . . .
3K - last updated 2005-12-23 14:30 UTC by server.cluster.mbg.gr
Raw TCP performance
Raw TCP is the fastest you can get. The following graphs show measurements of the raw TCP performance . . . TCP]] Following the addition of a new 30m long cable, aspera was directly connected with the main 24-port . . . the performance indicated by the graphs shown above is to be expected from machines that are otherwise . . .
2K - last updated 2004-10-31 17:39 UTC by NMG
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 . . . programmer said things like: DO 10 I=1 10 and ABEND They talked in capital letters, you understand. . . . 12-year old Pac-Man players (at very considerable salary savings). LANGUAGES The easiest way to . . . compilers. Real Programmers don't need all those abstract concepts to get their jobs done - they are . . . use to show their particular point of view invariably fit on a single page of some obscure journal or . . .
22K - last updated 2004-10-10 20:45 UTC by ppp1-68.axd.forthnet.gr
Removing global rotations-translations using selected atoms for fitting
If the structure contains flexible parts then things can go bad : the least squares superposition algorithm . . . the whole molecule and will happily move the stable part of the structure away from its correct position . . .
2K - last updated 2005-03-08 08:43 UTC by NMG
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 . . . the /work directory. * Create a file with a suitable name (like NAMD_job.sh) containing the following: . . .
5K - last updated 2005-06-30 07:19 UTC by glykos
Running a molecular dynamics simulation of native Rop
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . you do not do that you may end-up with questionable situations like this one : [[image: A wet hydrophobic . . . the files on your local machine, which probably isn't pc09. So, here comes the need for a cluster-wide . . . Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0.48 Info: HYDROGEN GROUP CUTOFF . . . 7 with 14006 kB of memory in use. Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 Info: COULOMB TABLE . . .
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 . . . 2000 ;# <===== CHANGE ME * The lines (in the above script) saying *cellBasisVector1*, *cellBasisVector2*, . . . the files on your local machine, which probably isn't pc09. So, here comes the need for a cluster-wide . . . Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0.36 Info: HYDROGEN GROUP CUTOFF . . . 7 with 4897 kB of memory in use. Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 Info: COULOMB TABLE . . .
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 . . . the files on your local machine, which probably isn't pc09. So, here comes the need for a cluster-wide . . . Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0.48 Info: HYDROGEN GROUP CUTOFF . . . 7 with 13567 kB of memory in use. Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 Info: COULOMB TABLE . . . 769 POINTS Info: NONZERO IMPRECISION IN COULOMB TABLE: 2.64698e-22 (712) 2.64698e-22 (712) Info: NONZERO . . .
30K - last updated 2005-09-27 12:04 UTC by server.cluster.mbg.gr
Running one of the Gromacs' benchmarks
* Download the [[gromacs lysozyme benchmark files.tar.gz]]. * Create a clean directory in /work/tmp and . . . the job started. * The Gromacs manual is available /via/ the cluster's homepage (documents -> . . .
2K - last updated 2005-04-13 13:38 UTC by glykos
SGE script to start a parallel job on the cluster
To run a parallel MPI program on the cluster : * Create a dedicated directory somewhere in /work * Place . . . needed by your job (and possibly also the executable) in this directory. * Create a file with a suitable . . .
2K - last updated 2004-10-12 09:53 UTC by server.cluster.mbg.gr
SGE script to start a simple (serial) job on the cluster
To submit a simple serial (ie non-parallel) job on the cluster via SGE do the following : * Create a . . . needed by your job (and possibly also the executable) in this directory * Create a file with a suitable . . . my_program_name with the name of your executable. Add (if needed) the arguments to your program. . . .
1K - last updated 2004-10-12 09:54 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 . . . detect when an animation frame changes trace variable vmd_frame($molid) w sscache return } # remove . . . the secondary structure assignments look resonable. * We now need to convert this information to . . . logo]] showing the secondary structure variability per sequence position : [[image: ss_logo image]] . . . Edit the ss_traj.dat file and use your macro-capable editor to ** Remove the frame-number column ** . . .
8K - last updated 2005-06-30 13:41 UTC by glykos
Spoel's thesis
Spoel is the writter of Gromacs. His thesis (on peptide simulations) is very nice (though rather old). . . . There is a copy of it available locally from here [http://server.cluster.mbg.gr/pdf/theses/Spoel_thesis.pdf] . . .
1K - last updated 2005-12-20 15:51 UTC by server.cluster.mbg.gr
Submitting jobs on the cluster, etc.
* Submitting jobs on the cluster : ** [[Running NAMD on the cluster via SGE]] ** [[SGE script to start . . . ** Grid engine's proper (and locally available) PDF documentation[http://server.cluster.mbg.gr/pdf/packages/SGE53AdminUserDoc.pdf]. . . .
1K - last updated 2006-03-23 17:27 UTC by server.cluster.mbg.gr
The MBG cluster for experienced users
Beware: incomplete work in progress ... == Prelude == The basic differences from a simple bunch of networked . . . needed to disallow job migration). * The availability of a proper (cluster-wide) queuing system (the . . . to have for large parallel jobs, but is probably too complex if you just want to run a simple stand-alone . . . on the ssh port (with X11 forwarding enabled). The implication is that if you are sitting . . . that box has an MBG address, then you should be able to connect to the server from your office (and . . .
6K - last updated 2006-10-05 12:31 UTC by server.cluster.mbg.gr
The Story of Mel, a Real Programmer
This was posted to Usenet by its author, Ed Nather (utastro!nather), on May 21, 1983. A recent article . . . language. Machine Code. Raw, unadorned, inscrutable hexadecimal numbers. Directly. Lest a whole new . . . be just arriving at the "read head" and available for immediate execution. There was a program to . . . find the next instruction. He coined an unforgettable term for this procedure. Although "optimum" is . . . an absolute term, like "unique", it became common verbal . . .
9K - last updated 2004-10-10 20:48 UTC by ppp1-68.axd.forthnet.gr
The Unix-Haters Handbook
This is a whole book available in the form of a PDF file[http:/pdf/misc/unix-haters.pdf] . . .
1K - last updated 2005-04-11 16:02 UTC by glykos
The current best explanation ...
I now think that the problem was not in userspace applications as implied by the discussion that follows. . . . not have the new kernel with the OOM killer enabled. The new kernel (shared by all other nodes) is . . . calculation-wise the server) appears to be stable. On a second thought, both this scenario and the . . .
3K - last updated 2005-02-14 09:56 UTC by NMG
Variance-covariance and cross-correlation analysis
/carma/ again : carma -v -cov -write CA.psf CA.dcd gv CA.dcd.varcov.ps carma -v -cov -dot -write CA.psf . . . x)}-1 \] where λ is an adjustable parameter determining the contrast. The following . . .
3K - last updated 2005-06-30 13:15 UTC by glykos
Why I write C
I would like to find the proper credit for the material below. Please mail me if you know the author. . . . back? Stroustrup: Actually, I was thinking about those days, just before you arrived. Do you remember? . . . so difficult to learn, that nobody would ever be able to swamp the market with programmers? Actually, . . . bound the two together so nicely. This would enable guys who only knew about DOS to earn a decent . . . Interviewer: What? Stroustrup: And as for 're-useable code' - when did you ever hear of a company re-using . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
4K - last updated 2004-06-17 11:19 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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
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 . . . and R. Clint Whaley, Innovative Computing Labs., UTK ===== An explanation of the input/output . . .
4K - last updated 2004-06-17 13:10 UTC by server.cluster.mbg.gr
αυτή τη σελίδα
= To see how these are produced, click 'edit text of this page' below = if you give up drinking, smoking . . . παραπάνω.. Testing typesetting capabilities (using LaTeX) : \[ \frac{ax^2+bx+c}{\Gamma(x)} . . . cos(xN)} \right] \] Testing matrix formatting capabilities : || this || is || a || || 3 || by || 3 || . . . smoke and fly? -the supafly- Testing graphing capabilities : <graph> digraph { n1 -> n2; n2 . . .
2K - last updated 2007-04-24 10:39 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 . . . of the angles are between 0 and 360 degrees. Probably /xplor/ will give values from -180 to 180. A way . . . The easiest method is to use a macro-capable editor to delete, say, all data points corresponding . . . 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute . . . 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' . . .
5K - last updated 2005-06-30 13:39 UTC by glykos
65 pages found.