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1) If you try to load a cpt and the "expected" directory defined by the path given in "output folder/molecule name" does not exist you get an error
2) On a MacBookPro, You start a simulation after a previous one ended or was cancelled and you do this without killing Zephyr but by going back to earlier tabs -- (with same or different molecule).
Then if you had "turned off" VMD on the previous simulation and now turn it on -- the VMD connection is not properly established. It will load the first frame into VMD and then continue the simulation without loading any additional frames. This will remain this way for any subsequent simulation done without quitting Zephyr.
3) None of the advanced parameters appear o be "linked" to the "Zephyr temperature parameter" .
4) On a MacBookPro, one cannot launch 2 "Zephyrs" -- this may be by design -- just an observation.
5) Normally when restarting Gromacs from the command line using a cpt file the "normal way" is to re-use the .tpr file from the stopped or crashed run. This results in re-using the same parameters. In Zephyr the default behavior is for these parameters to be overwritten with the initial (default) parameter values of Zephyr, if Zephyr is restarted.
I think when loading a cpt file one has to be able to optionally also load a tpr file. Ideally the Zephyr parameter screen would display the parameters in that tpr file -- giving the user the option to change them if they wish to do so.
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