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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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Drecated option, -DPOSRES in martinize script #418

Open junepark6 opened 2 years ago

junepark6 commented 2 years ago

In previous martinize.py(version: 2.5), positional restraint option supports '-DPOSRES', so that user can change the force constance in .mdp file, but the recent version of martinize2 does not contain this option. Could you provide this option in recent version?

pckroon commented 2 years ago

The -p option causes the generation of a [ position_restraints ] section, which looks like this:

[ position_restraints ]
#ifdef POSRES
  1 1 1000 1000 1000
...
#endif

The -pf option can be used to tune the force constant used (1000 default). This currently only supports floats.

So currently the -DPOSRES option you mention is implemented. Do you mean a -DPOSRESFC to tune the force constant in the itp/top file?

junepark6 commented 2 years ago

Yes, -DPOSRESFC option is very cool to me. I very appreciate for this update.

junepark6 commented 2 years ago

Does recent version include -DPOSRESFC option? If so, could you let me know how to use this? When I print a help message, but I can't find it.

pckroon commented 2 years ago

See also martinize2 -h. A -DPOSRESFC is not currently implemented besides the -pf option

fgrunewald commented 2 years ago

@pckroon this looks like a won't fix?

pckroon commented 2 years ago

Let's mark it up as a 1 banana improvement.