pyMDMix Activity
Molecular dynamics with aqueous-organic solvent mixtures
Status: Beta
Brought to you by:
d-alvarez
Activity for pyMDMix
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Daniel Álvarez posted a comment on ticket #1
Hi Amr, The scripts I used to generate all these boxes are completely outdated and...
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Amr Hamed created ticket #1
script to generate solvent mixture off file
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Mark J. Williamson committed [2de84a]
Default to default queue for the moment on Slurm
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Mark J. Williamson committed [c08480]
Ensure the correct number of eq steps are run w...
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Mark Williamson committed [db9d4a]
Correct minor typo
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Mark Williamson committed [710c9c]
First attempt at a Slurm template
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Mark Williamson committed [1dfa8f]
Add support for OpenMM in QueueWriting
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Added function to compute similarity to GridsMa...
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Forgot to add a trim function to ensure equal s...
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Fixed bugs in PDB magicFit alignment and grid c...
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Chenged MDprogram default to AMBER
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added getSimVolume to OpenMMCheck
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merging master
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corrections
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v0.2-1-gce113dc
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Create getSimVolume in Checkers and removed fro...
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pyMDMix released /pyMDMix-0.2.0.zip
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Added support for OpenMM (merged fork by Mark J...
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Modified documentation and minor bug
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Added CUBICBOX option to settings for choosing ...
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Improved solvent printing to include expected n...
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updated UPDATES, changed VERSION to 0.1.6 and m...
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Added create_min hotspot creation to build hots...
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bug
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Changed default to IWRAP=0 and added option in ...
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Take last completed production step to calculat...
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added UPDATE txt file
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added fixNumbering when retrieving Replica PDB....
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fixed residence hotspot type error
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debugged hotspotsmanager getHSbyID, id should b...
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Added trim function to mdmix tools
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Moved trim function to GridsManager and adapted...
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matplotlib legend prop={"size"} instead of prop...
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unstaged pyc files
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Daniel Álvarez García committed [64f9cb]
Minor formating bug in solvents.py and bug in d...
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Added exception handling in solvent off loading...
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Fixed error when loading old projects due to ch...
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Modified md-settings.cfg "nvt_prod_steps" becom...
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modified mdmix and Parses to allow creation of ...
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modified GridSpace to obtain list of loaded probes
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Modified SolvatedPDB to warn about non-recogniz...
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bug in process lambda function was removing pos...
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bug in last update
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Added stepselection to plot commands
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debugging check_com
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Daniel Álvarez García committed [b0bf85]
debugged check_com_tmp.txt
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fixed check_com_temp.txt, version compatible wi...
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fixed another dictionary comprehension for comp...
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modified check_com to test wether tmp0.pdb.1 (p...
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fixed check_com.sh that was ignoring ptraj inst...
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added masking of 999 points in hotspot calculation
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allow analysis to load action classess instead ...
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bug in GridData trim function fixed. Added chec...
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bug checking for ptraj instead of using variabl...
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Fixed bug in PDB string. Wrong column number fo...
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improved debugging info, fixed bug in hotspots ...
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typechange of mdmix link
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Merged master to correct align module bug
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fixed bug in align
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set warining to True in Replicas MD checking
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merged changes in master
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changed version number
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Added more flexibility to align command: now it...
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dbug
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dbug
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debugging
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Merge branch 'master' into correction
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Added setProductionSteps to replicas for easy c...
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bug fixed
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s
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s
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debugging correction
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debugging
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Daniel Álvarez García committed [382fdc]
debugging
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Daniel Álvarez García committed [2c6709]
fixed gridspace getvalues
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Daniel Álvarez García committed [dace51]
added changes in master to correction
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stuff
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Daniel Álvarez García committed [6dd117]
debug
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modified version number to 0.1.4
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fixed some bugs and improvements
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minor stuff
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Added multiprocessing to corrections, waiting f...
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debugged corrections in parallel
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Fixed bugs in PDB solvent detection and density...
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Fixed some errors in GridData and Replicas, Fin...
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problems commiting
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Daniel Álvarez García committed [0ec337]
Testing DensityAllHA
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Merge branch 'correction' of ssh://git.code.sf....
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Daniel Álvarez García committed [e7fd6d]
modified density
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Errors in project.cfg and added code to Density
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Changed hotspot centroid calculation to allow m...
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Initial commit
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