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New mek-quake. From Docswiki. This is a large cluster system to be used by the Wales and Vendruscolo groups.

As this is a new server, you will need to login once from each machine you use. ... log into the new repository to make sure it's working. svn ls $SVN/trunk.

PATHSAMPLE. From Docswiki. A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. PATHSAMPLE is documented here. Tutorials. These tutorials are under development. Please correct any

6. next step: creation new binary file points.min; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

A post script file with be saved as well as a new session file.

aux file from a latex compilation and creates a new bib file called references.bib which contains only the entries required by the corresponding.

up restart run in the current directory' echo 'Number of steps completed='$oldsteps echo 'Number of additional steps requested='$1 echo 'Total number of steps after restart='$steps # CREATING THE NEW ... Prints the top of the data file up to (but not

6. next step: creation new binary file points.ts; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

Where to put them. One can go on the new backup server but the primary ought to be close to the workstations.

In that sense, mercurial is very similar to the other new generation version management systems as git or bazaar. ... Also good. Since all new code that you write has bugs, you have a choice.

It is not meant to be a replacement for them, but rather as a playground for quickly testing new ideas, finding optimal parameters for the various routines in GMIN and OPTIM, ... You can also generate interactive disconnectivity graphs, which can be used

Unfortunately, the new version of the converter does not accept this and so you need to use the correct hex code instead in pstoimg.pin, #D9D9D9.

The ancient OpenPBS queueing system will be replaced with shiny new Torque (it'll look exactly the same to users, but work lots better behind the scenes).

Upgrading destiny. From Docswiki. Destiny is to be upgraded to SuSE and at the same time have a new disk installed to give a bigger /scratch and /usr/local.

For the new topology file, the energy is invariant to permutation of the aforementioned atoms or groups :). ... How do I use it? /perm-prmtop.py name-of-topology-file name-of-new-topology-file. Where can I find it?

Other IT stuff. From Docswiki. Made this page so I can provide links to older IT pages and not clutter up the 'headlines' on the front page. Retrieved from "". Navigation menu. Personal tools. Namespaces. Variants. Views. More. Navigation. Tools.

Maui compilation. From Docswiki. It's 7/6/06 at time of writing. On new mek-quake torque-2.1 does not work with current Maui because they have chnaged the

PATHSAMPLE then attempts to connect A and B and will repeat this until it finds a new minimum that reconnects A and B (this is however very unlikely to happen).

These have to be renamed in DMACRYS! UPDATE: the new PGI is slightly better, but as Davids recommends, don't use PGI! ... Moves via XML. This idea has been cancelled, use new Python interface instead I'm thinking of implementing a move protocol using an

It will contain tests of routines such as those in the new GMIN MOVES module.

It has a strong focus on an object oriented & modular design which makes it very powerful to try new functionality.

Please feel free to contribute new tests and to improve the old ones! ... If you are absolutely certain that your changes have made the code better, you should replace the expected_output folder with your new output files and commit the changes.

Running out of space on existing JBODs. Workstations tend to contain archives of old user accounts because new users need old users' data (or PI wants to hang onto it) but ... So we need a gigantic new JBOD to accomodate the growing data.

KNOPPIX_remastered | nice -5. /create_compressed_fs - 65536 > masterISO/KNOPPIX/KNOPPIX. Then boot up SuSE and copy the new compressed file over your old /KNOPPIX/KNOPPIX. ... Boot the knoppix system to test the new KNOPPIX file. Keep going round and

Computer Office services. From Docswiki. This has moved to the COs' wiki. COs only! And even more recently, this has gone public on (Raven password needed, but if you got here then you already have one). Retrieved from "". Navigation menu. Personal

Zippo Sicortex machine. From Docswiki. Please record useful notes about the new SiCortex machine here.

It should be omitted from new code. IARGC. subroutine iargc_subr(n) integer, intent(out) :: n.

Checkout the new repository and start writing the paper in the blank directory. ... else. All development should occur on branches. To create a new branch, run.

In short, a new parser is being developed by Kyle to allow the construction of a highly flexible move set. ... csw34> Temporary calls to new step taking routines for testing IF (NEWMOVEST) THEN!

I should find a concrete example that compares the old and new, but till I do that, here are some numbers for a calculation done on the new quad-core machine

We also issue a waring reminding users they need to reconfigure if they have module loaded a new compiler. # ... To add a new ban, find the list for the appropriate compiler in CMakeLists.txt, then copy the above example, changing the condition and

Adding a model to GMIN. From Docswiki. This is rough outline of the subrounties that need to be changed to add a new model to GMIN.

trunk) as follows:. svn copy url-old url-new. where, for example, url-old is $SVN/trunk and url-new is $SVN/branches/your-new-branch-name. ... 5 then new functionality exists to help you (see the SVN manual for more information).

Add stuff you'd like in the new image here. gaim (chat client). ... OpenOffice.org (Office suite). OpenSSH (SSH client). Pan (news client). Pine (mail/news client).

ajwt3/code/qchem/qcsetup.bash. H. 2. O test. create a new directory with the following files h2o.inp.

Eventually additions of new connections to the database will no longer reduce the rate constant.

Adding a model for PATHSAMPLE. From Docswiki. Under Construction. This is rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE. ... connectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466

If you add a new page to this wiki, please provide a link to it in the Comprehensive Contents Page under the section you think most appropriate. ... Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.

However, when you have the path.info file(s) from OPTIM you may not want to use them to start a new database -- instead, you can add them (one at a ... Systematically increasing the number of connections per minimum. Starting from an existing KTN, with

OpenSSH (SSH client) DONE. Pan (news client) DONE. Pine (mail/news client) DONE. ... rasmol (molecular visualisation) DONE. TeX/LaTeX (document preparation system) DONE. Thunderbird (mail/news client) DONE.

Copy the coords.prmtop and coords.inpcrd files you just made into a new directory, and add the following file:. ... For vacuum, use igb=0 and delete "saltcon" keyword. min_md.in - the AMBER (SANDER) settings for molecular dynamics (used to generate new

This gave me coords.inpcrd, coords.prmtop and perm.allow files for my new system. ... We should also include NATOMS_NEW which is the number of atoms in the system to which we are mutating.

svn/SCRIPTS/AMBER/symmetrise_prmtop/perm-prmtop.ff03.py coords.prmtop.old coords.prmtop. Assuming that worked without errors, you can then open up the new coords.prmtop file and change ... svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb

Mek-quake Queueing system. From Docswiki. Please write your thoughts about the mek-quake queueing system here. And please sign your posts! --Catherine 16:26, 21 June 2006 (BST). My thoughts are that what works best on most of the other clusters to

AMBERMUTFF ff - sets the force field for creating new topology files, ff is either 14 (ff14SB) or 99 (ff99SB). ... This effectively stops the AMBER part of GMIN and we initialise it from scratch with the new input files.

Here, we add a new target executable, OPEPGMIN, specifying that it requires the dummy sources, the added subdirectory OPEPinterface and the main gminlib library. ... Once this is done, the code should compile correctly with and without the new potential.

24663 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> $$$$$$ New timer profile $$$$$ List time 0.00959 Other: 0.00000 Electrostatic & VDW 0.00004 Other: 0.00000 Nonbond force 0.01572

Use the cmake option -DWITH_PYTHON. The goal of this interface is to allow for quick testing of new ideas before implementing them in Fortran.

Sorting a file by multiple columns. From Docswiki. If you have a file you want to sort using multiple columns of numbers, the sort command is your new best friend!

which adds /local/lib/python/site-packages to my PYTHONPATH (if the directory exists). This means I no longer have to worry about adding a new module to my PYTHONPATH.