Add the ability to generate BoreschRestraints via the pull code

[IAlibay]

As evidenced by the recent gmx redmine issue: https://redmine.gromacs.org/issues/2953, it may be prudent to implement a means of generating Boresch restraints that does not rely on the intermolecular_restraints code. This would allow us to leverage the pull code and help bring the .mdp files closer to those of the hardwall restraint simulations. It would also probably make the restraints easier to understand for new users.

This should be rather simple:

1. Generate a set of index groups using MDAnalysis which defines each of the 6 atoms involved in a Boresch restraint.
2. Generate a set of default .mdp options for the restraints.. something like:
   pull-group1-name = atom1
   pull-group2-name = atom2
   ... etc...
   pull-coord1-type = umbrella
   pull-coord2-type = umbrella
   .... etc ...
   pull-coord1-geometry = distance
   pull-coord2-geometry = angle
   ... for pull-coord3
   pull-coord4-geometry = dihedral
   ... for pull-coord[5-6]
   pull-coord1-init = [nm]
   pull-coord2-init = [deg]
   ... etc...

Ideally we can just provide this as a printed output for pasting into future mdp files and/or we can just create idealised template mdp files directly using this protocol.

[aniketsh]

Dear Irfan, This sounds great. Sincerely, Aniket

…

On Mon, May 20, 2019 at 3:24 PM Irfan Alibay ***@***.***> wrote: As evidenced by the recent gmx redmine issue: https://redmine.gromacs.org/issues/2953, it may be prudent to implement a means of generating Boresch restraints that does not rely on the intermolecular_restraints code. This would allow us to leverage the pull code and help bring the .mdp files closer to those of the hardwall restraint simulations. It would also probably make the restraints easier to understand for new users. This should be rather simple: 1. Generate a set of index groups using MDAnalysis which defines each of the 6 atoms involved in a Boresch restraint. 2. Generate a set of default .mdp options for the restraints.. something like: pull-group1-name = atom1 pull-group2-name = atom2 ... etc... pull-coord1-type = umbrella pull-coord2-type = umbrella .... etc ... pull-coord1-geometry = distance pull-coord2-geometry = angle ... for pull-coord3 pull-coord4-geometry = dihedral ... for pull-coord[5-6] pull-coord1-init = [nm] pull-coord2-init = [deg] ... etc... Ideally we can just provide this as a printed output for pasting into future mdp files and/or we can just create idealised template mdp files directly using this protocol. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA3HBARSSRBFAMZ3I6BPKALPWKRCNANCNFSM4HOB6MKA> .

-- Sincerely, Aniket Magarkar