Creating pull request to fix merge conflicts in my fork #2
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First incorporation of implicit solvent. Need to refine the code and test it on GPU.
(1) Skipped pdb4amber for now - otherwise there's disagreement in atom numbers between topology (pdb) and traj (dcd) files in MDAnalysis (2) small errors: eg implicit solvent model = HCT (not 'HCT')
Make ambertools work compatibly with others, particularly numpy. Lots of try-and-check. The order of those commands should (probably matter).
Bypass the cleanTraj function when using implicit solvent. Need to confirm if this is ideal: even without water and ions, is there still something worth cleaning?
1. Bypass the "particle coordinate is nan" issue by changing implicit solvent model from HCT to OBC1. Need to find out the detail. 2. Add a feature to skip 'do 2d analysis' and 'MMB', instead, start with a folded structure. 3. A few remaining issues: "extractFrame" of MD smoothing gave error of no unit cell dimension; cleanTraj and analyzeTraj: MDAnalysis seems confused by the pdb file (generated by MMB and processed in implicit solvent)
1. Add a few lines to and re-arrange opendna.py to allow a user to specify a chk file for resuming a MD simulation. Some decorative changes to main.py and interfaces.py too. 2. print_record() function in utils.py: add a parameter to specify the file path.
Use OpenMM PDBFile.writeFile() to save the last frame of the relaxed trajectory (MD smoothing): (1) OpenMM does not warn the lack of unit cell dimension (MDAnalysis does when fed with a structure + trajectory) -- perhaps not a good thing (2) The saved structure does NOT arouse "Non-optimal GB parameters detected for GB model" warning when using OBC1 or OBC2 implicit solvent. (3) Under HCT implicit solvent, the saved structure does NOT lead to "particle coordinate is nan" error in the following MD sampling step!!!
Add parameter "simTime=self.params['smoothing time']" to OpenMM class initialization during MDSmoothing. Before, MDSmoothing runs for the same length as MDSampling (runFreeApatmer).
Fixed the conflict between MMB program and OpenMM Python package on MacOS python environment, regarding the path to the .dylib files!
Allow users to resume previous sampling (MD sampling for free aptamer, not the MD smoothing yet) from the .chk file; This feature was completed and tested in the explicit solvent branch first; Have not tested them in implicit solvent yet.
(1) Went through all the parameters of prmtop.createSystem() when used for creating a simulation system in implicit solvent: implicitSolventSaltConc, soluteDielectric, solventDielectric, etc. Caution: no PBC in implicit solvent, therefore some non-bonded methods cannot be applied: PME, Ewald, LJPME. (2) freeImpATP_HCT.sh: an example job submission file.
"--impSolv=HCT" in the command line would pass HCT as a string, whereas createSystem() does not take a string but a class of HCT. Same for the other 4 supported implicit solvent models.
clean up some comments. Update the pipeline control of MD smoothing.
Added: params['skip smoothing']
Remove redundant comments and code
Update the example_sub.sh for local run
Update the main.py for local run
Update the opendna.py for local run
Update the interfaces.py for local run: change import statements regarding OpenMM
Update the pdbfixersource.py for local run: change import statements regarding OpenMM
Update the utils.py for local run: change import statements regarding OpenMM
Fix the links to bash files due to the change of repo name
Fix the situation when there is no docked structure found
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