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RashmiKumari / g_mmpbsa

MM-PBSA method for GROMACS. For full description, please visit homepage:
http://rashmikumari.github.io/g_mmpbsa/
GNU General Public License v3.0
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-pbsa should be switched on by default #8

Closed bieniekmateusz closed 6 years ago

bieniekmateusz commented 6 years ago

If I understand right, the main reason behind the existence of this package is the PBSA calculation. I've used your software naively just to realise that I only did the MM part later when I read the paper. But in some way this is very ironic and misleading that you can run software called mmpbsa and it by default only does not do pbsa. I believe this should be by default switched on.

rjdkmr commented 6 years ago

-pbsa used to be switched on by default during development phase. However, PB calculation could take lot of RAM and Processing. Therefore, this option acts as a check for user that they are starting PB calculation with correct parameters. Moreover, I do not expect that this tool should be used naively. At first, user should know about MM/PBSA theory before using this method. MM/PBSA comes with limitations and it cannot be used for every cases. Therefore, a literature reading is must before using this method.

Also, this is not an issue with g_mmpbsa code. Please post these type of questions to g_mmpbsa forum.

bieniekmateusz commented 6 years ago

This is an issue. It is confusing without any reason. You're implying that the "lots of processing" is a check for the user to know whether PB is running, which sounds like a terrible idea. Just because the software is slow at something that should not be used to convey other information.

You basically run "mmpbsa" and you have to tell the software to switch on pbsa. In that case you could have just call it "mm".

bieniekmateusz commented 6 years ago

Just to compare, you call the software "copy_and_paste" and by default turn off the "paste" part. The suggestion that the user always should be fully competent regarding the software even in the beginning is naive.

rjdkmr commented 6 years ago

This tool should not be used naively. There are lot of parameters which could be changed. For example, one do not run Gromacs mdrun without knowing about parameters in mdp files.

bieniekmateusz commented 6 years ago

No tool should be used naively. But that is not a reason to make something more confusing than it already is.