<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><br></div><div>Hi David, </div><div><br></div><div>As an easy practical workaround until a solution is implemented in gromacs itself, you can use the PLUMED plugin to apply restraints in a molecule-independent way. </div><div><br></div><div>Best, </div><div>Michel</div><div><br></div><div><br><blockquote type="cite"><div><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Sat, 22 Jun 2013 16:36:12 +0000<br>From: "Shirts, Michael (mrs5pt)" <<a href="mailto:mrs5pt@eservices.virginia.edu">mrs5pt@eservices.virginia.edu</a>><br>Subject: [gmx-developers] Re: free energy calculations with restraints<br>To: David Mobley <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>>, Discussion list for GROMACS<br><span class="Apple-tab-span" style="white-space:pre"> </span>development<span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>Message-ID: <CDEB4ABA.20FD9%mrs5pt@eservices.virginia.edu><br>Content-Type: text/plain; charset="us-ascii"<br><br><br>Looking through very briefly, I would think this should be possible to do<br>through the pull code. Basically, you could have an index group with 3 or 4<br>atoms, which can then be as angles or dihedrals.<br><br>Anyone with more expertise with the pull code who can comment further as to<br>whether this would work?<br><br>Best,<br>~~~~~~~~~~~~<br>Michael Shirts<br>Assistant Professor<br>Department of Chemical Engineering<br>University of Virginia<br><a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>(434)-243-1821<br><br><br><blockquote type="cite">From: David Mobley <dmobley@gmail.com><br></blockquote><blockquote type="cite">Date: Fri, 21 Jun 2013 13:44:25 -0700<br></blockquote><blockquote type="cite">To: Discussion list for GROMACS development <gmx-developers@gromacs.org><br></blockquote><blockquote type="cite">Cc: "Michael R. Shirts" <michael.shirts@virginia.edu><br></blockquote><blockquote type="cite">Subject: Re: free energy calculations with restraints<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Anyone have any insights on this? Do we need to think about implementing<br></blockquote><blockquote type="cite">angle/torsional restraints in the pull code, or can we re-cast the<br></blockquote><blockquote type="cite">restraints available within topology files to use absolute atom numbering?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Fri, Jun 14, 2013 at 12:47 PM, David Mobley <dmobley@gmail.com> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi, devs,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I'm writing with an issue relating to the interplay of new free energy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">features with restraints.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I'm very much appreciating some of the new free energy features in<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">gromacs, such as the 'couple-moltype' option which provides a way to set up<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">decoupling or annihilation of a specific molecule via free energy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">calculations without having to edit the topology file directly. This is<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">especially great when it comes to decoupling -- charge decoupling was not<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">previously possible via topology file editing, and vdW decoupling took<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">substantial manipulation of the topology file.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">However, for binding free energies, my work employs orientational<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">restraints between the protein and ligand. I need to be able to impose both<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">dihedral and angle restraints on angles between the protein and ligand.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Currently, I do this using angle-restraints and dihedral-restraints. This<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">requires that both the protein and ligand be within the same logical<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">'molecule', which (unfortunately) means that I can't make use of the new<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">free energy features above, since couple-moltype has to apply to a whole<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">molecule, not just part of a molecule.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">So, my I see two possible solutions to the problem, and hence have these<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">questions:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">1) Can dihedral and angle restraints be applied via the pull code? If not,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">are there any plans to add that?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">2) Alternatively, what about modifying the restraints code so it uses (or<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">at least optionally allows) absolute atom numbering, rather than numbering<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">within a specific molecule, thus allowing restraints (angle-restraints and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">dihedral-restraints) to be applied between 'molecules'?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">David<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">David Mobley<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">dmobley@gmail.com<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">949-385-2436<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">David Mobley<br></blockquote><blockquote type="cite">dmobley@gmail.com<br></blockquote><blockquote type="cite">949-385-2436<br></blockquote><br><br><br>------------------------------<br><br>-- <br>gmx-developers mailing list<br>gmx-developers@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-developers<br><br><br>End of gmx-developers Digest, Vol 110, Issue 29<br>***********************************************<br></div></blockquote></div><br><div>
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