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6 Jan 2021: New mek-quake. From CUC3. This is a large cluster system to be used by the Wales and Vendruscolo groups.

6 Jan 2021: New project ideas. From Raspberry Pi in the Chemistry Library. Share your ideas for projects using Raspberry Pis here:.

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.

6 Jan 2021: PATHSAMPLE. From CUC3. A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. PATHSAMPLE is currently documented for two versions, 2.0 and 2.1. Tutorials. These tutorials are under

6 Jan 2021: We also welcome new project ideas and recommendations for extra modules.

6 Jan 2021: It is robust tool, especially if you are starting of with a new set of code.

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

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

6 Jan 2021: Catherine 14:50, 28 March 2006 (BST). There is now an RSS feed for the sector IT news, providing updates of the messages of the day for the workstations and clusters.

6 Jan 2021: Where to put them. One can go on the new backup server but the primary ought to be close to the workstations.

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

6 Jan 2021: Other IT stuff. From CUC3. 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. Search. Navigation.

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

6 Jan 2021: 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.

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.

6 Jan 2021: Computer Office services. From CUC3. 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 tools

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.

6 Jan 2021: 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).

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).

6 Jan 2021: a symbolic link to the file's new location and leaving all other files untouched.

6 Jan 2021: DUMPINT 100 RESTORE GMIN.dump STEPS 15000 SAVE 100. The number of steps in the new data file should always be greater than in the original. ... In the new format, there is an extra line in the dump file which details the number of structures saved in the

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

In order to do so, new OPTIM keywords, DEBUG, DUMPNEBEOS, and DUMPNEBXYZ need to be added to print the NEB interpolated energy and coordinates in the files neb.xyz.31267.<n>,

New backup system. I want to buy a new backup server with about 6Tb of space, move the backups onto that, and make them user-accessible. ... New archive system. The other two old backup servers would immediately be free for reuse.

This is to be based on SuSE 10.3 as 11.0 is too new for compiler support. ... News reader. Pan (USENET is dying and the JANET news feed's days are numbered).

6 Jan 2021: new 4-index integral is.

Note that Google Reader has a delay in updating the feeds, so you won't see new logs up to an hour after they are created and are visible with Firefox. ... don't forget 'svn add <filename>' to schedule a new file for addition at the next commit!

6 Jan 2021: Upgrading destiny. From CUC3. 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.

DUMPINT 100 RESTORE GMIN.dump STEPS 15000 SAVE 100. The number of steps in the new data file should always be greater than in the original. ... In the new format, there is an extra line in the dump file which details the number of structures saved in the

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.

6 Jan 2021: As before, the calculations involve the new propagator module with the ALDAXCHF model. ... Compile on Tati with the new version of ifort and the ATLAS library.

6 Jan 2021: CamCASP/Programming/0. From CUC3. Status. Contents. Propagator. There have been major changes to the propagator modules. See Propagator for details. --alston 18:42, 5 May 2010 (BST). ENERGY-SCAN. What's working:. REDO_DF_ON_ROTATION =. TRUE. E1elst,

The new libraries are found in the AMBERTOOLS/dat/leap/lib directory, you will need to copy them to your AMBER version (AMBER12 or newer!). ... information), however leap generally prevents most clashes, so that a single minimisation generally is

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

To keep things organised, create a new directory in your current working directory (e.g FE_<THRESH>_<TEMP>) and copy the relevant output from the free energy calculation there. ... To construct the free energy disconnectivity graph you will need a 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.

6 Jan 2021: This will copy all code in SVN_code into a new directory called nosvn. ... It is quite low-profile: files are only copied if a new commit has been made and diffs are only generated for new commits.

6 Jan 2021: To create a new /.svndiffrc file, write $progname --create-rc >/.svndiffrc -c, --diffcmd x Use x as the diff command. ... item B<--create-rc> Send a configuration file example to stdout. To create a new F</.svndiffrc> file, write $progname --create-rc

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 Jan 2021: 1 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane.

The next step would be to simply merge the two pdb files such that the new pdb file contains information about only two strands which we are interested in. ... Paste these two parts one after the other into a new pdb file TGmismatch.pdb.

6 Jan 2021: odata.<n> -- OPTIM input file. odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM).

6 Jan 2021: Then someone's going to have fftw2 loaded and forget about it, and suddenly find they can't load a new compiler. ... A few months later I tried a variant of this by installing the new 64-bit cluster tardis without 32-bit Portland modules.

6 Jan 2021: transformation matrices with the factor <math>1/sqrt{(2l-1)!}</math> can be used as our new transformation to spherical GTOs is. ... Normalize the contraction blocks. Inclusion of normalization of spherical GTOs. Include the normalization coefficients of

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

6 Jan 2021: What have we done? There is a new line in the last section:.

6 Jan 2021: The new bits are the ENERGY-SCAN commands and those indicated by ''. The Skip MOs command is needed to get CamCASP to go on without reading in the molecular orbitals.

Making new local branches is completely trivial so you can easily work on two logically separate things (e.g. ... experimenting with a new potential in GMIN and adding a feature to disconnectDPS) at the same time within the same repository.