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Electronic Structure Group Meetings - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Electronic_Structure_Group_Meetings6 Jan 2021: Talks should last around 40 minutes to allow for discussion. Some of us are quite new or unfamiliar with certain areas, so perhaps a bit of background will help. ... Stephen Jenkins (surface science group). For any remarks, suggestions or new additions -
CHECKSPMUTATE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/CHECKSPMUTATEThis 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. -
CamCASP/Bugs/9 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Bugs/96 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. -
Setting up - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_upsvn/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 -
Installing python modules - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Installing_python_modules6 Jan 2021: 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. -
Mek-quake Queueing system - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Mek-quake_Queueing_systemMek-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 -
CamCASP/Programming/2 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/26 Jan 2021: new 4-index integral is. -
Mutational BH steps - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Mutational_BH_stepsAMBERMUTFF 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. -
SVN Page - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/SVN_Page6 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. -
Cmake interface building - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Cmake_interface_buildingHere, 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. -
ElaborateDiff - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/ElaborateDiff6 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 -
Calculating molecular properties - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_molecular_properties24663 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 -
CamCASP/Programming/0 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/06 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, -
Python interface for GMIN/OPTIM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Python_interface_for_GMIN/OPTIMUse the cmake option -DWITH_PYTHON. The goal of this interface is to allow for quick testing of new ideas before implementing them in Fortran. -
CamCASP/Programming/1 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/16 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 -
Sorting a file by multiple columns - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Sorting_a_file_by_multiple_columnsSorting 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! -
Installing python modules - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Installing_python_moduleswhich 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. -
Revamping the modules system - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Revamping_the_modules_system6 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. -
Wales Group Version control - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Wales_Group_Version_controlNote 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! -
CamCASP/Notes/7 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Notes/76 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. -
SVN setup - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/SVN_setupMaking 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. -
CamCASP/Notes/3 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Notes/36 Jan 2021: What have we done? There is a new line in the last section:. -
Local rigid body in OPTIM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Local_rigid_body_in_OPTIM3. Introduce new subroutines GENRIGID_IMAGE_CTORIGID and GENRIGID_IMAGE_RIGIDTOC in genrigid.f90. 4. Edit newneb.f90 - after initial interpolation, we do coordinate transformation to local rigid body. -
CamCASP/Programming/7 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/76 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. -
SuSE 10.3 workstation image - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/SuSE_10.3_workstation_imageThis 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). -
Biomolecules in PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Biomolecules_in_PATHSAMPLEThe 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 -
Managing interactive jobs on cluster - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Managing_interactive_jobs_on_clusterpressing Shifto opens a new window with several options along with the corresponding letter that needs to be pressed to sort the top window based on a particular column. -
ElaborateDiff - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/ElaborateDiffTo 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
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