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OPTIM and PY ellipsoids tutorial - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/OPTIM_and_PY_ellipsoids_tutorialIf you are unsatisfied with the topology, it's time to try a new connection scheme. ... permissions? JOBSPERNODE/PBS vs CPUS again? "Operation not permitted". "error code returned by host stdio - 1." -> close the terminal and open a new one! -
Connecting Sub-databases - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Connecting_Sub-databasesThis new reorganised file we give the rather unimaginative name of lowest_to_highest_distances_tot. ... Assuming all of the connections were successfully made, all we need to do now is to merge these new connected databases together. -
Notes on MINPERMDIST - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Notes_on_MINPERMDISTThe best permutation is returned in the LPERM array. SAVEPERM is set to NEWPERM with the new permutation applied. ... Updates to permutation vector and coordinates (l870-l912). ALLPERM is updated with the new swaps. -
Symmetrising AMBER topology files - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Symmetrising_AMBER_topology_filesjob). Also, it would be helpful once you've done this if you add your new cofactor to the group8 list. -
Basic linux commands everyone should know! - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Basic_linux_commands_everyone_should_know!mkdir. mkdir newdir newdir2. This will create two new directories, newdir and newdir2. -
Environment modules - CUC3
wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Environment_modules6 Jan 2021: If you do module avail after loading the use.own module, you'll see there's a new section: /home/${USER}/privatemodules. -
Mercurial - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/MercurialIn 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. -
Calculating order parameters - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_order_parametersCHARMM to calculate the order parameters charmm_new < order_parameters.inp > charmm.out. -
Using GMIN to generate endpoints (CHARMM) - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_GMIN_to_generate_endpoints_(CHARMM)Setting up CGMIN. Copy the metenk.crd file you have just created into a new directory, and rename it input.crd. ... We now need to create a new file, data, which contains the GMIN keywords we would like to use. -
Running a G\=o model with the AMHGMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Running_a_G%5C%3Do_model_with_the_AMHGMIN1 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane. -
Running Wales Group software on Windows 7 - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Running_Wales_Group_software_on_Windows_7New packages can be selected later by running the setup wizard again. -
Removing minima and transition states from the database - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Removing_minima_and_transition_states_from_the_database6 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, -
Biomolecules in the energy landscape framework - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Biomolecules_in_the_energy_landscape_frameworkThe new libraries are found in the AMBERTOOLS/dat/leap/lib directory, you will need to copy them to your AMBER version (AMBER12 or newer!). -
Using BHINTERP to find minima between two end points - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Using_BHINTERP_to_find_minima_between_two_end_points6 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, -
Creating movies (.mpg) of paths using OPTIM - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Creating_movies_(.mpg)_of_paths_using_OPTIM6 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 -
Using VMD to display and manipulate '.pdb' files - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Using_VMD_to_display_and_manipulate_%27.pdb%27_files6 Jan 2021: Formyl. Vinyl. Chloride. Hydroxyl. Methyl. Those you can start a new molecule from are:. -
Loading OPTIM's min.data.info files into PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Loading_OPTIM%27s_min.data.info_files_into_PATHSAMPLEmin.data.info.initial. In a new directory copy the following files:. coords.inpcrd, coords.prmtop, min.data.info.initial, perm.allow, pathdata. -
GMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMINThe program knows many different empirical potentials, and it is straightforward to add new systems. ... symmetry.f. mdiff is used to test whether a generated symmetry operation is new. -
Removing minima and transition states from the database - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Removing_minima_and_transition_states_from_the_databaseFirst 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, -
Getting started with SLURM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Getting_started_with_SLURMChange 'jwrm2' to your own username. We copy only the files GMIN needs in order to run, then change to the new directory. ... the files back and adds new stationary points to the database, then deletes the temporary directory.
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