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Adding a model to GMIN - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Adding_a_model_to_GMIN6 Jan 2021: finalio.f -- generates output. --mp466 00:24, 8 July 2008 (BST). Retrieved from "". Navigation menu. Personal tools. ... Navigation. Tools. This page was last edited on 8 July 2008, at 00:24. -
Fixing thunderbird links - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Fixing_thunderbird_linksNavigation. Tools. This page was last edited on 13 May 2019, at 13:24. -
Raspberry Pi in the Chemistry Library:About - Raspberry Pi in the…
https://wikis.ch.cam.ac.uk/library-pi/wiki/index.php/Raspberry_Pi_in_the_Chemistry_Library:About6 Jan 2021: 01223 336329, 24 hours in advance, so we can ensure that someone is available to lend it to you. -
CamCASP/Notes/8 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Notes/86 Jan 2021: Navigation. Tools. This page was last edited on 31 May 2010, at 19:24. -
Adding a model to GMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_a_model_to_GMINfinalio.f -- generates output. --mp466 00:24, 8 July 2008 (BST). Retrieved from "". Navigation menu. Personal tools. Namespaces. Variants. Views. More. Search. -
CamCASP/ToDo/diskIO - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/ToDo/diskIO6 Jan 2021: 31 lineq_solver_lu 23 3422.38 matrix_read 187396 17104.03 <--- lineq_lu_iter 25 3182.26 matvec_types 9482 3451.95 energy_scan 1 59787.24 df_int 40294 -
Simulations using OPEP - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Simulations_using_OPEP4 2.137 5.757 -0.745 ATOM 24 OXT GLU 4 3.977 5.797 -1.795 END. ... ichain.dat contains all fragments of the system. 1 1 24. scale.dat contains the scaling information for the potential. -
CamCASP/Numerical - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Numerical6 Jan 2021: fun! DC -24.50340 9.09293 -0.02501 0.01275 -18.94748 0.05356 ===============================================================================. I can't believe the aQZ/MC result. ... 7426 -3.8415 -6.3363 24.1369 0.6432 0.5905 -19.5499 ====================== -
Adding a model for PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_a_model_for_PATHSAMPLEconnectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466 00:24, 8 July 2008 (BST). -
Adding a model for PATHSAMPLE - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Adding_a_model_for_PATHSAMPLE6 Jan 2021: connectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466 00:24, 8 July 2008 (BST). -
CamCASP/ToDo/diskIO - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/CamCASP/ToDo/diskIO187396 17104.03 <--- lineq_lu_iter 25 3182.26 matvec_types 9482 3451.95 energy_scan 1 59787.24 df_int 40294 26046.73 make_oneeint 9480 2970.26 DIaux 7110 -
Mek-quake Queueing system - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Mek-quake_Queueing_system6 Jan 2021: This can be reduced if we have problems. --Catherine 17:44, 24 August 2006 (BST). -
Decoding heat capacity curves - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Decoding_heat_capacity_curvesNavigation. Tools. This page was last edited on 15 November 2022, at 14:24. -
Electronic Structure Group Meetings - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Electronic_Structure_Group_Meetings6 Jan 2021: Navigation. Tools. This page was last edited on 24 February 2014, at 18:33. -
DisconnectionDPS - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/DisconnectionDPS6 6 -1.8455167037 5823.9083945062 1 2 24 -12.6466356094 5826.9370977040 1 6 17. -
Setting up - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up2.342 -3.160 ATOM 23 CE1 PHE 2 11.834 2.503 -2.025 ATOM 24 HE1 PHE 2 12.406 1.886 -2.704 ATOM 25 CZ PHE 2 ... 23 CE1 PHE 2 9.287 0.851 -0.692 ATOM 24 HE1 PHE 2 9.205 -0.191 -0.412 ATOM 25 CZ PHE 2 9.580 1.203 -
Compiling GMIN with CHARMM - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Compiling_GMIN_with_CHARMM6 Jan 2021: Navigation. Tools. This page was last edited on 14 July 2008, at 11:24. -
Using GMIN to generate endpoints - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_GMIN_to_generate_endpointsNavigation. Tools. This page was last edited on 24 May 2011, at 16:19. -
Conversion between different data file formats - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Conversion_between_different_data_file_formats6 Jan 2021: Navigation. Tools. This page was last edited on 7 October 2008, at 17:24. -
Intel Trace Analyzer and Collector - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Intel_Trace_Analyzer_and_CollectorNavigation. Tools. This page was last edited on 13 May 2019, at 13:24. -
Running a Go model with the AMHGMIN - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Running_a_Go_model_with_the_AMHGMIN6 Jan 2021: 1uama 1uama 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 -
Mek-quake Queueing system - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Mek-quake_Queueing_systemThis can be reduced if we have problems. --Catherine 17:44, 24 August 2006 (BST). -
CamCASP/Programming/7 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/76 Jan 2021: Energies in kJ/mol elst ind2C disp2C exch exind2C exdisp2C becke100.out -28.499 -10.832 -9.971 24.756 5.624 1.670 becke10.out -28.499 -10.829 ... 964 24.756 5.622 1.669 becke3.out -28.499 -10.829 -9.962 24.756 5.622 1.668. -
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/api.php?hidebots=1&ur…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/api.php?hidebots=1&urlversion=1&days=7&limit=50&action=feedrecentchanges&feedformat=atomMediaWiki 1.35.13 https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php?title=Git_Workflow&diff=1816&oldid=1813 Git Workflow 2024-07-22T20:24:21Z <p></p> ... as of 20:24, 22 July 2024</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 127:</td> <td -
GMIN MOVES module - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMIN_MOVES_moduleCsw34 17:24, 14 April 2014 (UTC). Retrieved from "". Navigation menu. -
Finding an initial path with OPTIM and starting up PATHSAMPLE…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Finding_an_initial_path_with_OPTIM_and_starting_up_PATHSAMPLE_(CHARMM)144.0096582 5.4996 -149.5092547 24.935 17.263 1.969 24.372 18 -149.5092547 0.11279E-01 -149.4979756 3.8322 -153.3301944 6.223 5.891 -
CamCASP/Notes/3 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Notes/36 Jan 2021: Step 0.75 B! Grid exp Colour-map 0 210 0.25 1 6 240 0.75 1 12 300 1.0 0 18 360 0.75 1 24 390 -
Calculating binding free energy using the FSA method - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_binding_free_energy_using_the_FSA_methodPAC A 317 17.578 25.580 63.751 1.00 15.05 C ATOM 2564 C1' PAC A 317 17.351 24.336 62.935 1.00 22.49 C ... 00 15.05 H ATOM 0 H2' PAC A 317 19.077 24.466 61.823 1.00 24.42 H. -
https://wikis.ch.cam.ac.uk/ro-walesdocs/images/c/c7/OTV.prepin.txt
https://wikis.ch.cam.ac.uk/ro-walesdocs/images/c/c7/OTV.prepin.txt3 Mar 2016: 1.608 117.636 42.409 -0.13223 23 C1 c B 22 19 14 1.445 121.657 165.337 0.90383 24 O1A o E 23 22 19 -
REMD with AMBER - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/REMD_with_AMBER6 Jan 2021: Navigation. Tools. This page was last edited on 24 October 2008, at 13:48. -
Running a Go model with the AMHGMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Running_a_Go_model_with_the_AMHGMIN1uama 1uama 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 -
CamCASP/Interfaces - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Interfaces6 Jan 2021: ICUT=24 $END $SYSTEM MEMORY=220000 $END $GUESS GUESS=HCORE $END $DATA Ar in ArHF 86 functions, acpVDZ basis: monomer A, DCBS C1 Ar 18.0 0.0 0.0 -
Using AMBER 14 on the GPU and compute clusters - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_AMBER_14_on_the_GPU_and_compute_clustersNavigation. Tools. This page was last edited on 13 May 2019, at 10:24. -
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: mp466 02:05, 24 October 2008 (BST). Retrieved from "". Navigation menu. -
STARTING INITIAL PATH JOBS WITH PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/STARTING_INITIAL_PATH_JOBS_WITH_PATHSAMPLEpathdata:. GCORES '-c8'. SYSTEM X. EXEC /svn/OPTIM/builds/ifort_64_2019_5_281/OPTIM. NATOMS 24. SEED 1. -
Global optimization of biomolecules using CHARMM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Global_optimization_of_biomolecules_using_CHARMM0.00000 23 3 GLY H 3.90715 0.75613 0.00000 1 3 0.00000 24 3 GLY CA 3.92458 2.87358 0.00000 1 3 0.00000 25 ... 12 12 13 13 14 17 19 19 20 20 22 20 21 17 18 22 24 24 25 25 27 25 26 22 23 27 29 29 37 37 39 -
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_databasemp466 02:05, 24 October 2008 (BST). Retrieved from "". Navigation menu. -
Calculating rate constants (GT and fastest path) - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Calculating_rate_constants_(GT_and_fastest_path)6 Jan 2021: 2100556 Dijkstra> MFPT for fastest path: A<-B value= 0.7030943368E25 B<-A value= 0.2425804971E-08 Dijkstra> rates without conditional probability: A<-B value= 0.1422284248E-24 B<-A value= ... 412234294.2 Dijkstra> rates with conditional probability: A<-B -
Submitting jobs, interactively or to a cluster queue system - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Submitting_jobs,_interactively_or_to_a_cluster_queue_systemthe shortest walltime is 24 hours on Volkhan). The third line tells PBS to execute commands from the current working directory from which you submitted the job. ... SBATCH -n 24 # # then # srun -N1 -n1 /sharedscratch/wales/PATHSAMPLE.pgi/PATHSAMPLE > -
Computing CHARMM FF energy using GMIN, MMTSB and CHARMM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Computing_CHARMM_FF_energy_using_GMIN,_MMTSB_and_CHARMM0.0000000000 24 2 ALA HB3 4.4074251611 4.5080096993 1.2139617347 DIALA 2 0.0000000000 25 2 ALA C 5.7914561039 2.3986507715 0.0000000000 DIALA 2 0.0000000000 26 ... NGRP NST2 0 1 0 4 1 0 6 1 0 10 1 0 14 1 0 16 1 0 20 1 0 24 1 0 26 1 0 1! -
Git Workflow - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Git_WorkflowNavigation. Tools. This page was last edited on 22 July 2024, at 21:24. -
Adding partially finished OPTIM stationary points to a PATHSAMPLE…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_partially_finished_OPTIM_stationary_points_to_a_PATHSAMPLE_databaseNavigation. Tools. This page was last edited on 10 May 2019, at 18:24. -
Generating parameters using AMBER's built in General Forcefield…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Generating_parameters_using_AMBER%27s_built_in_General_Forcefield_(gaff)Navigation. Tools. This page was last edited on 13 May 2019, at 10:24. -
Notes on MINPERMDIST - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Notes_on_MINPERMDISTNotes on MINPERMDIST. From Docswiki. The subroutine that must not be named. Bringing of headaches. Bane of Friday afternoons. Mother of alignment algorithms. This page aims to collect useful information on how MINPERMDIST works to assist in the -
Connecting Sub-databases - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Connecting_Sub-databases00003_00303 670 811 connectlowest> Distance: 24.67395896. Error creating thumbnail: Unable to save thumbnail to destination. -
Generating pdb, crd and psf for a peptide sequence - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Generating_pdb,_crd_and_psf_for_a_peptide_sequenceNATOM 1 ALAD 1 ALA CAY 24 -0.270000 12.0110 0 0.00000 -0.301140E-02 2 ALAD 1 ALA HY1 3 0.900000E-01 1.00800 0 0.00000 ... 0.900000E-01 1.00800 0 0.00000 -0.301140E-02 11 ALAD 1 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02 12 ALAD 1 ALA -
Calculating rate constants (GT and fastest path) - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_rate_constants_(GT_and_fastest_path)2100556 Dijkstra> MFPT for fastest path: A<-B value= 0.7030943368E25 B<-A value= 0.2425804971E-08 Dijkstra> rates without conditional probability: A<-B value= 0.1422284248E-24 B<-A value= ... 412234294.2 Dijkstra> rates with conditional probability: A<-B
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