exercises:2015_cecam_tutorial:forcefields
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exercises:2015_cecam_tutorial:forcefields [2015/09/01 21:12] – mwatkins | exercises:2015_cecam_tutorial:forcefields [2015/09/01 21:39] – mwatkins | ||
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Enter the 4 character accession code of a protein, here I've put in ubiquitin - 1ubq - and select load into a new molecule. You should now see a line representation of the protein in the vmd window. The important step is now to generate a topology for this molecule that defines how it is connected and will define how interactions from the main forcefield we will use will be mapped to the atoms in the molecule we have just downloaded. To do this we can use the autopsf plugin. We select this from the " | Enter the 4 character accession code of a protein, here I've put in ubiquitin - 1ubq - and select load into a new molecule. You should now see a line representation of the protein in the vmd window. The important step is now to generate a topology for this molecule that defines how it is connected and will define how interactions from the main forcefield we will use will be mapped to the atoms in the molecule we have just downloaded. To do this we can use the autopsf plugin. We select this from the " | ||
+ | | ||
+ | Hit I'm feeling lucky. You should now have three new files in the directory where you started VMD (or maybe where it is installed in windows if you haven' | ||
+ | |||
+ | We can easily solvate this in VMD using the " | ||
+ | |||
+ | {{http:// | ||
+ | | ||
+ | Now you should have solvate.psf and solvate.pdb in your directory, which contain the coordinates and connectivity information of the solvated protein. For some proteins you might now need to add ions into the solvent to neutralize the system, but we're OK with ubiquitin. | ||
+ | |||
+ | At this point we're nearly ready to run CP2K. First we need to get hold of the forcefield files. The CHARMM forcefields are distributed from the MacKrell group website {{http:// | ||
+ | |||
+ | OK, finally ready to go. The first thing to do is to carry out a rough minimization to remove any close contacts between the protein and the waters that we added in VMD. These clashes would probably make molecular dynamics unstable if we just started running. | ||
+ | |||
+ | < | ||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | #this assumes that you've downloaded and extracted the file as instructed | ||
+ | parm_file_name toppar/ | ||
+ | parmtype CHM | ||
+ | &SPLINE | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | &EWALD | ||
+ | EWALD_TYPE spme | ||
+ | ALPHA .44 | ||
+ | GMAX 36 | ||
+ | O_SPLINE 6 | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC 40.685 42.380 46.291 | ||
+ | &END CELL | ||
+ | & | ||
+ | COORD_FILE_NAME solvate.pdb | ||
+ | COORDINATE pdb | ||
+ | CONN_FILE_FORMAT psf | ||
+ | CONN_FILE_NAME solvate.psf | ||
+ | &END TOPOLOGY | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | &GLOBAL | ||
+ | PROJECT ubiquitin_mini | ||
+ | RUN_TYPE GEO_OPT | ||
+ | &END GLOBAL | ||
+ | &MOTION | ||
+ | & | ||
+ | MINIMIZER LBFGS | ||
+ | #just do 100 steps, | ||
+ | #we only want to remove bad contacts | ||
+ | MAX_ITER 100 | ||
+ | &END | ||
+ | &END MOTION | ||
+ | </ | ||
+ | |||
+ | Now we can start to equilibriate the system in MD | ||
+ | |||
+ | < | ||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | parm_file_name toppar/ | ||
+ | parmtype CHM | ||
+ | &SPLINE | ||
+ | | ||
+ | | ||
+ | &END | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | &EWALD | ||
+ | EWALD_TYPE spme | ||
+ | ALPHA .44 | ||
+ | GMAX 36 | ||
+ | O_SPLINE 6 | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC 40.685 42.380 46.291 | ||
+ | &END CELL | ||
+ | & | ||
+ | COORD_FILE_NAME solvate.pdb | ||
+ | COORDINATE pdb | ||
+ | CONN_FILE_FORMAT psf | ||
+ | CONN_FILE_NAME solvate.psf | ||
+ | &END TOPOLOGY | ||
+ | |||
+ | & | ||
+ | | ||
+ | &END | ||
+ | &END | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | &GLOBAL | ||
+ | PROJECT ubiquitin_md | ||
+ | RUN_TYPE MD | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | RESTART_FILE_NAME ubiquitin_mini-1.restart | ||
+ | RESTART_DEFAULT F | ||
+ | RESTART_POS T | ||
+ | &END EXT_RESTART | ||
+ | |||
+ | &MOTION | ||
+ | &MD | ||
+ | ENSEMBLE NVT | ||
+ | STEPS 1000 | ||
+ | TIMESTEP 0.5 | ||
+ | TEMPERATURE 298 | ||
+ | & | ||
+ | | ||
+ | TYPE CSVR | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | &END | ||
+ | &END MD | ||
+ | &END MOTION | ||
+ | </ | ||
+ | |||
+ | We take the coordinates from previous minimization run using the external restart option in CP2K. Hopefully this works for you and you can explore the MD facilities in the code. |
exercises/2015_cecam_tutorial/forcefields.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1