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Debugging odd transition states in OPTIM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Debugging_odd_transition_states_in_OPTIMIn 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>, -
Restarting a GMIN run from a dump file - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Restarting_a_GMIN_run_from_a_dump_fileDUMPINT 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 -
Short 'awk' examples - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Short_%27awk%27_examplesPlease notify me if you find errors or new commands to add to this list (total length under 65 characters). -
Creating mismatched DNA duplex using NAB - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Creating_mismatched_DNA_duplex_using_NABThe 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. -
Constructing Free Energy Disconnectivity Graphs - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Constructing_Free_Energy_Disconnectivity_GraphsTo 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 -
Revamping the modules system - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Revamping_the_modules_systemThen 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. -
Using the implicit membrane model IMM1 - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_the_implicit_membrane_model_IMM11 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane. -
Comprehensive Contents Page - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Comprehensive_Contents_PageCan be very useful for visualizing your system and for rapidly implementing and testing new ideas. ... rough outline of the subroutines that need to be changed to add a new model to GMIN. -
CamCASP/Releases - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Releases6 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. -
List of output files for PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/List_of_output_files_for_PATHSAMPLEodata.<n> -- OPTIM input file. odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM).
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