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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:.

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.

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.

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.

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.

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

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).

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

6 Jan 2021: new 4-index integral is.

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.

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,

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

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

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

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.

6 Jan 2021: Needs commands. SET NEW-PROP KERNEL-EPS 0.00001 END BEGIN POLARIZABILITY MOLECULE <name> NEW-PROP. ... Can now be used in energy routines. Just add NEW-PROP to the commands.

6 Jan 2021: First off back up the directory. The minima specified in files min.remove and ts.remove are removed and new files min.data.removed, ts.data.removed, min.A.removed,

6 Jan 2021: Aux basis: aTZ Basis type as indicated. New mid-bond set used: 3s3p3d2f1g.

6 Jan 2021: If you do module avail after loading the use.own module, you'll see there's a new section: /home/${USER}/privatemodules.

6 Jan 2021: Often they are initial and final structures of studied path or reaction (however, here reaction means geometrical change in the system, not breaking and forming new bonds). ... overwrite! Update: new version of PATHSAMPLE does not overwrite this file,

6 Jan 2021: Formyl. Vinyl. Chloride. Hydroxyl. Methyl. Those you can start a new molecule from are:.

6 Jan 2021: 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: If this doesn't help, then the NEWCONNECT commands in odata will tell OPTIM to try to bridge the gap by finding new TSs in the usual way to form a

6 Jan 2021: If you have more than one new residue, just load frcmod and prepin files for each of them.

6 Jan 2021: It can be found by going to File >> New Molecule and then browsing for the topology file you need. ... Then check the file type carefully, the new version of VMD automatically assumes that mdcrd files are not periodic, so if your coordinate file is

6 Jan 2021: Maui compilation. From CUC3. 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

6 Jan 2021: 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.

6 Jan 2021: Files min.[A,B,data].fastest, ts.data.fastest,points.[min,ts].fastest: a new database containing only the stationary points on the fastest path. ... connect them, and all the individual stationary points in those groups will be written to new.

6 Jan 2021: 2. Sample section of the input for a charmm run:. OPEN UNIT 20 FORM NAME protein_new.pdb READ! ... Excuse the lack of docu for this program ;-) Then paste the new coordinates into your newly-made.

6 Jan 2021: export AMBERHOME=/home/$USER/svn/AMBERTOOLS. Exit vi and then source the file you just altered to export the new variable:. ... Old $PATH:. export PATH=$PATH:/home/csw34/scripts. New $PATH. export PATH=$PATH:/home/csw34/scripts:$AMBERHOME/exe. Once you

6 Jan 2021: 5.5-dev. Branched from trunk on the 25-Mar-10. New program: res2disp added. ... Kernel integrals constructed in CamCASP. New propagator module: Implements the ALDA(X) kernel in the manner described in Bukowski et al.

6 Jan 2021: 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.

6 Jan 2021: to save the ligand you are editing as a new PDB using File>Save and changing the type to. ... R<CILE 385> Created a new atom named: O2 within residue:. R<CILE 385> Added missing heavy atom:.

6 Jan 2021: This information is used to set up UCS computer accounts in advance and is needed for any new member of staff.

6 Jan 2021: 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?

6 Jan 2021: General queueing problems. From CUC3. This page is for general queueing discussion. There are specific pages for discussing mek-quake and tardis. I have moved the paragraph from the page for me-quake as it is more appropriate here. --Catherine 09:55,

6 Jan 2021: perl -pi -e 's/old string/new string/' list_of_files. is equivalent to. for file in list_of_files; do sed -e 's/old string/new string/' $file > tmp mv

6 Jan 2021: Adding a model to GMIN. From CUC3. This is rough outline of the subrounties that need to be changed to add a new model to GMIN.

6 Jan 2021: 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.

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