<div dir="ltr"><div><div><div><div>Hi, devs,<br><br></div><div>I'm writing with an issue relating to the interplay of new free energy features with restraints.<br></div><div><br></div>I'm very much appreciating some of the new free energy features in gromacs, such as the 'couple-moltype' option which provides a way to set up decoupling or annihilation of a specific molecule via free energy calculations without having to edit the topology file directly. This is especially great when it comes to decoupling -- charge decoupling was not previously possible via topology file editing, and vdW decoupling took substantial manipulation of the topology file.<br>
<br>However, for binding free energies, my work employs orientational restraints between the protein and ligand. I need to be able to impose both dihedral and angle restraints on angles between the protein and ligand. Currently, I do this using angle-restraints and dihedral-restraints. This requires that both the protein and ligand be within the same logical 'molecule', which (unfortunately) means that I can't make use of the new free energy features above, since couple-moltype has to apply to a whole molecule, not just part of a molecule.<br>
<br></div>So, my I see two possible solutions to the problem, and hence have these questions:<br>1) Can dihedral and angle restraints be applied via the pull code? If not, are there any plans to add that?<br></div>2) Alternatively, what about modifying the restraints code so it uses (or at least optionally allows) absolute atom numbering, rather than numbering within a specific molecule, thus allowing restraints (angle-restraints and dihedral-restraints) to be applied between 'molecules'?<br>
<br></div>Thanks!<br>David<br><br clear="all"><div><div><div><div><div><div><div><br>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>949-385-2436<br>
</div></div></div></div></div></div></div></div>