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2006-05-11
eisagwgh shmeiwsewn radioviologias b etous(3) eisagwgh 2hs ergasthriakhs askhshs Genetikhs II . . .
1K - last updated 2006-05-11 09:39 UTC by server.cluster.mbg.gr
2006-11-21
Εισαγωγή σημειώσεων Μορ.Νευροβιολογίας + δημοσιεύσεις . . . Ekfrashs+simatodotisis" KEfALAIO 28 "METADOSH SHMATON" (28STUDENTS.pdf) . . .
1K - last updated 2006-11-21 08:49 UTC by server.cluster.mbg.gr
2007-12-13
eisagogi ergastiriakon paradoseon embruologias, moriakis kuttarikis biologias gia 3 etos kai texnikon . . .
1K - last updated 2007-12-13 10:22 UTC by server.cluster.mbg.gr
2007-12-17
min vazete simeiwseis an den adeiasei prwta o diskos C apo tis simeiwseis twn palaioterwn etwn. . . .
1K - last updated 2007-12-18 09:36 UTC by server.cluster.mbg.gr
2008-10-22
EVALA TIS DIALEXEIS PHYSIOLOGY_1 MEXRI KAI THN DIALEXH 5-6 KAI TEXNIKES MORIAKHS BIOLOGIAS_1 THN PRWTH . . . OPOIA PITHANON THA ALLAXEI OTAN TELEIWSOYN OI PARADOSEIS AYTHS . . .
1K - last updated 2008-10-22 10:42 UTC by server.cluster.mbg.gr
2008-12-05
This is Gus. Evala diafaneies apo emvriologia kai moriaki viologia anapti3is(11-13) kai moriaki neurologia . . . (mathima 6). Adeiasa ton kado anakuklwsis(eixe diafaneia fusiologias . . .
1K - last updated 2008-12-05 13:51 UTC by server.cluster.mbg.gr
2009-01-16
New day rises for the new students... We had plenty of them today... I'm not so optimistic for their . . . but there may be light at the end of the road... Me Costas a.k.a Gus imported cell biology at . . . dancing all together! One more windoze machine dead today! It was a lethal day for this thing. Well, . . .
1K - last updated 2009-01-16 16:09 UTC by server.cluster.mbg.gr
2009-04-02
Evala dialexeis 2 & 3 tis domikis_1. Evala tis eikones apo tin PCR twn omadwn 1 kai 2 tou prwtoy . . .
1K - last updated 2009-04-02 14:08 UTC by server.cluster.mbg.gr
2009-11-04
Exoun mpei ta dyo prwta frontistiria toy mathimatos efarmoges moriakis biologias stis epistimes ygeias. . . . dialexeis toy k. skavdi gia drosophila,to fylladio twn ergastiriwn. . . .
1K - last updated 2009-11-05 13:08 UTC by server.cluster.mbg.gr
2009-11-05
Sto deytero etos, exoun mpei oi diale3eis Fysiologias I (Introduction to Physiology, Membrane Physiology) . . . Ubuntu Box oso kai sto 10. Episis, epeidi o synadelfos 3exase na to anaferei x8es, yparxoun kai oi . . .
1K - last updated 2009-11-05 13:16 UTC by server.cluster.mbg.gr
2009-11-26
Exoun mpei sto 4o etos oi simeiwseis Radioviologias gia to akadimaiko etos 2009-2010 kai i Yli. . . .
1K - last updated 2009-11-26 13:24 UTC by nefeli.mbg.duth.gr
2009-12-16
Exoun mpei: 4o_etos:Oles oi dialexeis Iologias. Neurobiology: exoun mpei oi dialexeis 5-10. 3o_etos:Embryology: . . . 4-11 kai panida tis elladas Φυσική στις Βιολογικές Επιστήμες:Dialexi . . .
1K - last updated 2009-12-16 16:48 UTC by nefeli.mbg.duth.gr
2010-11-01
Kalo mina kai kalo akadimaiko e3amino se olous! Kai twra ta typika: Sto trito etos exoun perastei: ~ . . .
1K - last updated 2010-11-01 08:44 UTC by nefeli.mbg.duth.gr
2010-12-21
Exoun mpei oi dialexeis radiobiologias, oi dialexeis 8 kai 9 tis moriakis neurobiologias kathws kai oi . . .
1K - last updated 2010-12-21 14:30 UTC by pc17.cluster.mbg.gr
A linux virus ...
See http://math-www.uni-paderborn.de/~axel/bliss/ for the whole story ... Subject: Re: [masq] 1st virus . . . statements about this are, at best, misleading. To quote from their web site: McAfee (Nasdaq: . . . MCAF), the world's leading vendor of anti-virus software, today announced . . . We encourage concerned Linux users to download a free working evaluation copy of our VirusScan . . . you. Linux doesn't need a virus checker; Linux administrators need to use some basic intelligence . . .
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 . . . the relevant parts of a useful discussion I've had on the NAMD mailing list. The gist is that that . . . may vary'). Note that if you follow Marc's advice (Message 2 below) the total simulation time . . . though, it is probably better to follow Marc's advice. == Message 1== From glykos@mbg.duth.gr Tue . . . The initial minimisation (down to a 'GRADIENT TOLERANCE: 1.0179') and heating stage appeared . . .
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 . . . there is no turning back. Ok, now that you had your cup of coffee : * Make an easy start : go to . . . as shown below. PLEASE NOTE : if you have made restarts during your simulation, then there will . . .
7K - last updated 2005-06-23 09:07 UTC by glykos
Backup, backup, backup ... using the server's DVD
Read first the [[Backup, backup, backup ...]] section, then come back. ---- You can only use the server's . . .
3K - last updated 2005-11-30 15:45 UTC by server.cluster.mbg.gr
Benchmarking and scale-up
For trivially parallel problems (running, for example, many independent instances of the same program . . . (for example, the NAMD runs shown below), instead of trying to guess its real-life performance from . . .
2K - last updated 2009-02-17 20:18 UTC by ppp1-31.axd.forthnet.gr
Broadcasts (constant N, NB)
===== HPLinpack 1.0a -- High-Performance Linpack benchmark -- January 20, 2004 Written by A. Petitet . . .
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 . . .
1K - last updated 2004-10-19 14:25 UTC by natasa.biology.uoc.gr
Calculation of eigenvalues and eigenvectors
/carma/ it is : carma -v -cov -eigen -write -proj 1 10 1 CA.dcd CA.psf head -10 carma.eigenvalues.dat . . .
1K - last updated 2005-06-17 08:32 UTC by glykos
Calculation of frame-to-frame rmsds
NOTE WELL : calculation of the rms deviation between each and every frame of two DCD files can be a lot . . . is an example (which assumes that you've already created a CA-only PSF file) : carma -v -fit native.psf . . .
1K - last updated 2005-03-08 09:51 UTC by NMG
Calculation of rmsd from the average structure
/xplor/ to save the day : structure @native.psf end coordinates disposition=comp @aver_and_rms.pdb evaluate . . . ($step = 1) evaluate ($current = $first) read trajectory asci=false input=fitted.dcd begin=$first . . . evaluate ($current =$current + $step) read trajectory next end end loop traj stop Then use . . .
2K - last updated 2005-06-30 13:06 UTC by glykos
Calculation of rmsd from the starting structure
If you've used /carma/ to remove translations-rotations, then you already have seen a plot of the evolution . . . " D " native.psf native.dcd mv carma.fit-rms.dat AD.dat carma -fit -atmid "ALLID" -segid " B " -segid . . . mv carma.fit-rms.dat A.dat xmgr ALL.dat AD.dat BC.dat A.dat giving something like : [[image: . . . ($step = 1) evaluate ($current = $first) read trajectory asci=false input=native.dcd begin=$first . . . $rms evaluate ($current =$current + $step) read trajectory next end end loop traj stop where *starting.pdb* . . .
2K - last updated 2005-06-30 13:02 UTC by glykos
Calculation of the average structure and corresponding fluctuations
/xplor/ saves the day : structure @native.psf end dynamics analysis average asci=false input=fitted.dcd . . . removed. Edit aver_and_rms.pdb and remove the header lines. Save the modified file. The B-factor column . . .
1K - last updated 2005-06-30 13:03 UTC by glykos
Calculation of the evolution of the radius of gyration
/xplor/ it is : structure @native.psf end evaluate ($first = 0) evaluate ($step = 1) evaluate ($current . . . = $first) read trajectory asci=false input=fitted.dcd begin=$first . . . $rg1 $RG evaluate ($current =$current + $step) read trajectory next end end loop traj stop and then . . . gyration.list -bxy 1:2 -bxy 1:3 [[image: radius of gyration evolution (xmgr)]] ------ You can . . .
1K - last updated 2005-06-30 13:07 UTC by glykos
Calculation of water and ion distributions
The object of the exercise is to generate a map showing the distribution of waters (hydration pattern) . . . density map, the difference being that instead of electron density it will show average water (or . . . of the map to a minimum. You can artificially add the first frame from heat_out.dcd to an existing . . . Z : -10.98 15.87 2.44 26.85 ** You will have to add a border around it, so in this example the limits . . . of the map to a minimum. You can artificially add the first frame from heat_out.dcd to an existing . . .
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*. . . . n = 460*460), 460, 460, byrow = TRUE) Read 211600 items > hc <- hclust( dist(A), method="complete" . . . clusters you have and then you can use a more advanced clustering method to define them (note however . . . n = 460*460), 460, 460, byrow = TRUE) Read 211600 items > library(cluster) > f <- . . .
6K - last updated 2005-10-13 11:08 UTC by P.S. Georgoulia
Comments on 2004-06-03
Creation date :-) -- Anonymous 2004-10-02 14:15 UTC ---- Add your comment here. -- Anonymous 2004-10-02 . . . 14:15 UTC ---- Add your comment here. -- Anonymous 2004-10-02 14:16 . . .
1K - last updated 2004-10-02 14:16 UTC by server.cluster.mbg.gr
Comments on 2007-11-23
Add your comment here.uparxoun dialekseis fusiologias 1 gia to deutero etos -- Anonymous 2007-11-23 10:04 . . .
1K - last updated 2007-11-23 10:16 UTC by server.cluster.mbg.gr
Comments on OperatorsPage
Add your comment here. mpike to kefalaio 29 sti Diakyttariki gia trito kai tetarto etos -- katerina 2004-11-10 . . .
1K - last updated 2004-11-16 11:52 UTC by server.cluster.mbg.gr
Comparison of sets of eigenvectors
If you have two independent trajectories (or, two independent pieces from the same trajectory), you may . . . follows implements the above equation. It will read a specified number of eigenvectors from two files, . . . argv[1] ); exit( 1 ); } } k1++; } printf("Read %d vectors, each of length %d from file %s\n", n, . . . argv[2] ); exit( 1 ); } } k2++; } printf("Read %d vectors, each of length %d from file %s\n", n, . . .
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 . . . here that on some occasions in may be advantageous to keep crystallographically determined . . .
2K - last updated 2004-10-11 09:26 UTC by server.cluster.mbg.gr
Details for each project
||project||initial pdb||psfgen||minimization||psfgen||solvation/ionization||box size & center|| ||native_qb||1o9y.pdb->remove . . . use molecular dimensions boundary: 2.4A box padding: 15A, Cfinal=0.1M NaCl x Na & y Cl were . . . added, charge before=-20e, charge after=1|| ||native_flin||1o6a.pdb->remove . . . - || - ||Cfinal=0.1M NaCl, 14 Na & 7 Cl were added, charge before=-7e, charge after=2.5||(89.96, . . . 66.47, 64.84) & (3.27, -1.29, -0.76)|| ||AD_dimer|| ||BC_dimer|| ||T40I_qb|| ||T40Y_qb|| ||T40W_qb|| . . .
1K - last updated 2004-09-30 13:40 UTC by natasa.biology.uoc.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 . . . few eigenvectors. This you do with /xmgr/ (read block data with columns 1-2, or 1-3, or 1-4, ..., . . . } exit(0); } </source> The program will read a file containing pairs of coordinates of points . . .
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 . . . with a clean PDB of your structure. PyMol can add missing hydrogens and side chains (?), but you . . . Location*. The APBS binary location should already be there (/usr/local/bin/apbs). Add the location . . .
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, . . . NBMINs (4,8) * NDIVs (2,3) * RFACTs (0,1,2) * Broadcasts (0,1,2,3,4,5) * Lookahead (0,1) HPLinpack . . . 1 2 RFACTs (0=left, 1=Crout, 2=Right) 6 # of broadcast 0 1 2 3 4 5 BCASTs (0=1rg,1=1rM,2=2rg,3=2rM,4=Lng,5=LnM) . . . 2 # of lookahead depth 0 1 DEPTHs (>=0) 2 SWAP (0=bin-exch,1=long,2=mix) . . .
28K - last updated 2004-06-29 11:31 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 . . . waste people's time telling them things they already knew. It's more efficient just to give them the . . . it might be a sign of good things. A throbbing headache is not a good thing, but it can be a sign of . . . consciousness after being hit on the head. Variation in wealth can be a sign of variation . . . in productivity. If you have a tribe of nomads collecting sticks for a fire, how much more productive . . .
29K - last updated 2005-05-30 15:25 UTC by glykos
HPL benchmarks (9 nodes)
The 9 nodes are the server (Pentium IV) and the 8 newest nodes (Celerons). The mpich library and executables . . . Initial tests : * [[icc, mpich, gcc-made cblas]] * [[icc, mpich, intel math kernel library]] . . . best seems to be NB=100. Stick to that. * [[Broadcasts (constant N, NB)]] BlongM (BCAST=5) looks best. . . . 60. * [[NBmin]] 8 looks better * [[Look-ahead depth]] set to 0 * [[Final test with respect to . . .
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 . . . HrcQb protein is sensitive to proteolysis and had resisted all crystallization attempts. However, . . .
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 . . .
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. * . . . Several disks ready for last rites ? (pc6, pc13, pc15). == November . . . Weather getting cold, start few jobs ,-) * PC2 dead for good. Pooh. == June 13th, 2007 == * Everything . . . everything off. * The water spraying exercise had its toll: server's UPS misbehaving (replace battery . . . & overload lights). == May 22nd - June 7th, 2007 == * Electrical . . .
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) . . . graphs for FliN 4mer]] * Simulation of the AD HrcQb dimer ** [[Heating-up NAMD script for HrcQb . . . 2mer]] **[[Average rmsd for each residue]] **[[Radius of gyration]] . . .
2K - last updated 2004-10-19 14:04 UTC by natasa.biology.uoc.gr
My job on mpi slow doesn't start
If you submitted a job on the mpi_slow (parallel) queue and your job doesn't start, check the contents . . . as a master queue. The way to avoid pc15 is to add the following line in your SGE qsub script : #$ . . .
1K - last updated 2005-03-28 13:08 UTC by glykos
NAMD benchmarks and scaling-up
The tests were performed with a 59428-atom system, identical with the one used for the [[Molecular dynamics . . . room which is connected with the cluster via an additional hub. The result is that for this node the . . .
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 . . . connection of node number 9 (aspera) involved an additional hub. This significantly changed the effective . . . for two reasons (i) communication overhead, (ii) because of the FFT used for the electrostatics . . . + celerons). Another way to show that it is advantageous to submit two independent jobs is the . . .
5K - last updated 2004-07-08 14:05 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 . . .
2K - last updated 2005-02-05 15:02 UTC by NMG
Performing a molecular dynamics simulation in a hexagonal cell
Using an orthogonal cell for a periodic boundary simulation of a cylindrically-shaped molecule is one . . . that (i) you do a DNA run, and, (ii) you've already done the Dickerson tutorial ]. When using VMD's . . . /solvate/ pluggin, instead of ... # # Make water box # solvate psfgen_ions.psf . . .
3K - last updated 2005-06-30 12:41 UTC by glykos
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 . . . or ask NMG for a copy of his paper-made models. With so much of an introduction, preparing . . . the way the solvent box is being build. Instead of building the water box by adding a rim of waters . . . near the surface of the unit cell is low, leading to significant negative pressures at the beginning . . .
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 . . . performance of the program, a comparison was made between running Qs with a simple 'mpirun' command, . . .
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). . . . these days. For all examples that follow please add a '-trace' flag to tell /carma/ to draw a backbone . . . /vmd/. The problem is that /vmd/ attempts to load the whole trajectory file in memory. With the limited . . . MBytes the following will happen : * As /vmd/ reads data from the disk (and onto physical memory), . . .
3K - last updated 2005-12-23 14:30 UTC by server.cluster.mbg.gr
Radius of gyration
* Radius of gyration as a function of frame **[[plot1]]: the radius of gyration is calculated for the . . .
1K - last updated 2004-10-19 16:23 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 . . . These graphs also show the pronounced effect of adding a (hub) or, worse, a (switch + hub) on a connection . . . graphs of raw TCP]] Following the addition of a new 30m long cable, aspera was directly . . .
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 . . . faced today with a world in which little old ladies can get computers in their microwave ovens, 12-year . . . and a Real Programmer. If this difference is made clear, it will give these kids something to aspire . . . isn't worth doing. STRUCTURED PROGRAMMING The academics in computer science have got into the "structured . . . world. My first task in the Real World was to read and understand a 200,000-line FORTRAN program, then . . .
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 . . .
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 . . . you should log to pc13 (and nowhere else). * Adjustment of the job's priority (so that the machines . . . remain responsive) had to be done manually on each node. * There was no . . . to set an upper limit to the total machine load, or used memory, etc). = The new way = Enter SGE . . . $TMPDIR/charmlist cat $TMPDIR/charmlist # # Ready ... # /usr/local/NAMD_2.5/charmrun /bin/mosrun . . .
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 . . . ----- If you are seriously into peptides, do read [[Spoel's thesis]] ----- ----- === Peptide PDB generation . . . of inertia : #!/bin/tcsh -f # # This will read a PDB file and rotate/translate it so that # 1. . . . << eof /usr/local/xutil/moleman2.lib REad FPGF.pdb XYz ALign_inertia_axes WRite aligned.pdb . . . the PDB file created by moleman, remove the header, give all atoms a chain identifier (e.g. 'A'). . . .
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 . . . ./ * Download the Rop dimer from PDB [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1ROP] . . . the following : #!/bin/tcsh -f # # This will read a PDB file and rotate/translate it so that # 1. . . . << eof /usr/local/xutil/moleman2.lib REad dimer.pdb XYz ALign_inertia_axes WRite aligned.pdb . . . /A.pdb/ and retain only the A-chain coordinates. Add an _END_ at the end of the file. Find-and-replace . . .
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 . . . ./ * Download the B1 domain of protein G from the PDB [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1PGB] . . . _ATOM_ or _TER_. Also, retain the final _END_. Add a chain identifier for all atoms of the monomer, . . . the following : #!/bin/tcsh -f # # This will read a PDB file and rotate/translate it so that # 1. . . . << eof /usr/local/xutil/moleman2.lib REad proteinG.pdb XYz ALign_inertia_axes WRite aligned.pdb . . .
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 . . . ./ * Download the coordinates for Dickerson's dodecamer from PDB . . . the following : #!/bin/tcsh -f # # This will read a PDB file and rotate/translate it so that # 1. . . . << eof /usr/local/xutil/moleman2.lib REad ddoc.pdb XYz ALign_inertia_axes WRite aligned.pdb . . . /A.pdb/ and retain only the A-chain coordinates. Add an _END_ at the end of the file. Repeat for /B.pdb/. . . .
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 . . .
2K - last updated 2005-04-13 13:38 UTC by glykos
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 . . . with the name of your executable. Add (if needed) the arguments to your program. * Submit . . .
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 . . . for the given molecule number and frame already # exists in the Tcl array sscache_data(molecule,frame). . . . the frame-number column ** Remove spaces ** Add fasta-format identifiers inbetween successive lines. . . . ) abs_scale = 800.0 / rel_scale; printf("%%!PS-Adobe\n"); printf("%%%% From ss_plot.\n"); printf("/M . . . frame ); printf("{ currentfile DataString readhexstring pop }\nfalse 3\ncolorimage\n"); count = . . .
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 . . . exactly *between* the Cβ and Cγ atoms (instead of its normal tetrahedral position). The tetrahedral . . .
2K - last updated 2006-04-11 14:20 UTC by server.cluster.mbg.gr
Submitting an interactive job with qmon doesn't work
This is because the node that the job gets submitted to cannot open a window on the machine you work . . . machine on this planet. Consider using (instead of /qmon/'s 'interactive job') the command /qtcsh/ . . .
1K - last updated 2004-10-03 21:11 UTC by ppp1-9.axd.forthnet.gr
Submitting jobs on the cluster, etc.
* Submitting jobs on the cluster : ** [[Running NAMD on the cluster via SGE]] ** [[SGE script to start . . . . . .
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 . . . is not always a nice thing to have (the overhead associated with continuously moving a job around . . . the nodes makes migration a bad idea for long jobs, see below for the commands needed . . . DNS for the LAN is offered by the head node which is the 190.100.100.100 machine (server.cluster.mbg.gr). . . . ..., with aliases pc1, pc2, ... The head-node also serves as a http-proxy-server (running . . .
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 . . . devoted to the macho side of programming made the bald and unvarnished statement: Real Programmers . . . write in FORTRAN. Maybe they do now, in this decadent era of Lite beer, hand calculators, and "user-friendly" . . . sounded funny and Real Computers were made out of drums and vacuum tubes, Real Programmers . . . even, assembly language. Machine Code. Raw, unadorned, inscrutable hexadecimal numbers. Directly. . . .
9K - last updated 2004-10-10 20:48 UTC by ppp1-68.axd.forthnet.gr
The current best explanation ...
I now think that the problem was not in userspace applications as implied by the discussion that follows. . . . Instead, my current best explanation shifted to kernel space . . . nodes) is same version and everything, but the addresses of the system calls are different. So, my . . . is that NAMD hits the different server kernel address space and this is what causes the problems. . . . installed on server (and a new initrd image made). Testing it will have to wait for a reboot. * . . .
3K - last updated 2005-02-14 09:56 UTC by NMG
Tools and methods for analysing MD simulations
Please add other analyses, other methods/programs for performing the same task, etc. * [[Quick view of . . . * [[Calculation of the evolution of the radius of gyration]] * [[Calculation of the average . . .
2K - last updated 2007-02-05 10:15 UTC by server.cluster.mbg.gr
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 . . . \frac{2}{1+\exp(-\lambda x)}-1 \] where λ is an adjustable parameter determining the contrast. The . . .
3K - last updated 2005-06-30 13:15 UTC by glykos
What to do if your work dies...
Your work has unexpectedly died. Don't worry, it happens most of the times. There will always be someone . . . should be the /heat/ and /equi/ directories you had made. Create a new /restart/ directory. * Copy at . . . and do the following: *** at the input files add an option below /coordinates/ named as /bincoordinates/ . . . subdirectory in /restart/. * Now you are ready to submit your job by typing *qsub NAMD.sh*. . . .
2K - last updated 2004-11-19 15:14 UTC by P.S. Georgoulia
Why I write C
I would like to find the proper credit for the material below. Please mail me if you know the author. . . . the interview, the interviewer got more than he had bargained for and, subsequently, the editor decided . . . competent - I stress the word 'competent' - graduates at a phenomenal rate. That's what caused the . . . it only just ran on those Sun 3/60 things. They had all the ingredients for what I wanted. A really . . . to do. Stroustrup: OK, so this new language had to divorce itself from Unix, by hiding all the system . . .
12K - last updated 2004-09-28 15:47 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 . . .
3K - last updated 2004-06-16 08:50 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 . . . otherwise the physical memory will not be adequate. The easiest method is to use a macro-capable . . . n = 3217*2), 3217, 2, byrow = TRUE) Read 6434 items > library(cluster) > p <- pam( . . .
5K - last updated 2005-06-30 13:39 UTC by glykos
76 pages found.