search

Martini-Force-Field-Initiative / Bartender

Automated bonded parameters for Martini 3
GNU Lesser General Public License v3.0
14 stars 0 forks source link

input files #5

Closed WillPPK closed 8 months ago

WillPPK commented 8 months ago

Hi,

Just a suggestion - but a sample input (.inp) file would really be appreciated as it is quite hard to write from scratch - if you know what I mean..

Thanks a lot!

Will

rmera commented 8 months ago

Hey!

The problem is that the input file is very system-dependent.
There is a sample in the Wiki: https://github.com/Martini-Force-Field-Initiative/Bartender/wiki and also a script in the release package, inside the utils/ directory that will create the input file for you, though it requires a Gromacs ndx file (for the mapping) and an itp file with the bond terms you want parametrized.

WillPPK commented 8 months ago

I suggest you put wiki on the README - ideally first few lines so that a dumb person like me knows that it exists. Most people don't bother writing one that's why...

I see - maybe make a folder called example? even if it is system-dependent, but if you can create input from gmx itp and ndx then that's worth noting!

ricalessandri commented 8 months ago

@WillPPK in the meantime, please see this tutorial chapter (open-access), section 1.2.7, that explains how to generate the input in detail, incl. a reference to the write_bartender_input.py util that @rmera mentioned.

WillPPK commented 8 months ago

Also - what's the mapping ndx supposed to look like? Is it like this?

[ R1 ]
  16   19
[ R3 ]
   6    8   10
[ R2 ]
  15   18
[ R4 ]
   5    9
[ R5 ]
   4   12   14
[ R6 ]
   7   11   13   20
[ R7 ]
   1    2    3   17
WillPPK commented 8 months ago

By the way - the book chapter looks amazing and I will make my students read them! Thanks a lot for the hard work.

ricalessandri commented 8 months ago

Glad to hear the chapter is useful. Regarding the index file you posted, that looks like a plausible gromacs index file for mapping an all-atom structure to 7 CG sites.

rmera commented 8 months ago

Those are good suggestions, thanks!

@ricalessandri could you add a small page on the write_bartender_input.py to the wiki please? I don't think we are in a hurry with that, but it would be nice.

@GilbertoPPereira, I could add one of the test systems, say, PET, with a -very- reduced trajectory to the main repo as an example. Let me know if you want a particular system there (PET is the one I have available here).

WillPPK commented 8 months ago

Any would do - thanks! PET would be nice.

Ps. I will ask several questions as I go along - so if other users come - they can get help..

Pss. I just try to see if this is better than my hand-made parameter.

GilbertoPPereira commented 8 months ago

I think you can add the PET version you have. It changed from there till now, but it should work. Otherwise, naphtalene from Riccardos' paper works very nicely as a tutorial.

WillPPK commented 8 months ago

Thanks a lot!