Comments (6)
First point done.
Tutorial [1] cleaned and small formatting/bug solved. Commit: j3mdamas/htmd@a1ca92c002dd01fca840a1dca5ea33fd3bc55ec6
Tutorial [2] also cleaned and reformatted. Some parts of tutorial [2] were removed because they were redundant with tutorial [1]. A small section on Molecule.insert
was moved from [2] to the appropriate part in [1]. I did not test the trajectories section, I did not have one to test. Commit: j3mdamas/htmd@f89e372b32884a1e0375b586cbe1216be373f386
Second point is ongoing. @giadefa, it may not be ready for Thursday, but we'll see.
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Second point done. Commit: j3mdamas/htmd@18a91da930ed26270d0fb685e10c8a8017cdbbe8
More redundancies were removed. The tutorial is also Slide-mode ready. It's a bit clunky in that mode, because of a RISE issue (damianavila/RISE#188), but it works.
@giadefa is possibly going to use it on the Masters classes tomorrow, and if he thinks its OK, it may replace tutorials [1] and [2] in the future.
EDIT: the trajectory section is now tested too.
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I think the new tutorial was adopted. Tutorials [1] and [2] deleted. Point 3 postponed.
Commit: j3mdamas/htmd@701f4ac81af59bafb0b52fc971913a3e62e85e7a
Issue closed.
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Beyond adopting it we should also put it online no? :D So I guess we should pull it to the multiscalelab fork and then make a new doc publishing
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@giadefa I guess we need to first do a pull request from @j3mdamas fork into acellera and then pull from the acellera repo into our multiscalelab fork. Can you do it?
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Gianni already did it, but using my file directly instead of pulling from
my branch. It's alright but I'll need to fix the website because it's buggy
on the menus.
On Apr 14, 2016 6:45 PM, "Stefan" [email protected] wrote:
@giadefa https://github.com/giadefa I guess we need to first do a pull
request from @j3mdamas https://github.com/j3mdamas fork into acellera
and then pull from the acellera repo into our multiscalelab fork. Can you
do it?—
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Reply to this email directly or view it on GitHub
#11 (comment)
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Related Issues (20)
- Tutorial adaptative sampling HOT 4
- acemd is failing with cuda version 12.1 HOT 1
- Error : model.viewStates(nucleic=True), not recognize the 'nucleic' parameter HOT 5
- MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. HOT 4
- Issue with model._active_set HOT 1
- charmm build in htmd 2.3.8 HOT 3
- Parameters generated with charm.build on HTMD
- IndexError: arrays used as indices must be of integer (or boolean) type HOT 6
- Trouble installing: htmd does not exist HOT 2
- Provide simlist with single .psf file for all trajectories HOT 1
- Reg : Amber / Charmm Force field parameters for ARG (mono-methyl, dimethyl (asym, sym) HOT 4
- Installation Error: acemd >=2019.01.24 , which does not exist HOT 2
- acemd Computation: atomRestraint harmonic caused external energy calculation HOT 2
- Extract Trajectory Without Water and Ions HOT 1
- inconsistent results for ACEMD 2 and ACEMD 3 HOT 19
- unable to execute the tutorial HOT 2
- Request to Fix Error with 5-Methyl Cytosine amber Force Fields and Suggestion for Improvement HOT 15
- Constant ratio for membrane protein simulations HOT 1
- ERROR: syntax error in file "parameters", line number 15733: syntax error in CHARMM nbfix
- problem in the systemPrepare function with new version
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