Hi, Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is used at end of the complex topology file. This is a bug? >From my first mail:
> I think [ dihedral_restraints ] will be the same as [ dihedrals ] because > the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are > taken as 0 (zero), right? Checked also the position of the ligand during the simulation on the VMD. It is very mobile in the decoupled state as I said in the previous mail. *First test:* [ intermolecular_interactions ] [ bonds ] ; ai aj type bA kA bB kB 1391 2615 6 0.654 0.0 0.654 4184.0 [ angles ] ; ai aj ak type thA fcA thB fcB 1393 1391 2615 1 88.8 0.0 88.8 41.84 1391 2615 2614 1 32.9 0.0 32.9 41.84 [ dihedrals ] ; ai aj ak al type thA fcA thB fcB 1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84 1393 1391 2615 2614 2 122.6 0.0 122.6 41.84 1391 2615 2614 2610 2 12.8 0.0 12.8 41.84 *Second test:* [ intermolecular_interactions ] [ bonds ] ; ai aj type bA kA bB kB 1391 2615 6 0.654 0.0 0.654 4184.0 [ angles ] ; ai aj ak type thA fcA thB fcB 1393 1391 2615 1 88.8 0.0 88.8 41.84 1391 2615 2614 1 32.9 0.0 32.9 41.84 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 1410 1393 1391 2615 1 -159.7 0.0 0.0 -159.7 0.0 41.84 1393 1391 2615 2614 1 122.6 0.0 0.0 122.6 0.0 41.84 1393 1391 2615 2614 1 12.8 0.0 0.0 12.8 0.0 41.84 On 10 November 2017 at 22:36, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/10/17 2:21 PM, Ahmet Yildirim wrote: > >> Dear users, >> >> I add the following [ intermolecular_interactions ] section into the >> topology file of protein-ligand complex for free energy calculations. >> Unfortunately this setting doesn't provide me what I want in the decoupled >> state. The ligand in the decoupled state is very mobile compared to the >> coupled state. It means that the conformational sampling of the ligand in >> the decoupled state is quite different from the coupled state. That is not >> expected of course. Any suggestions as to why this might be? >> >> Do you think that there is something wrong with the following settings, >> e.g. [ dihedrals ] part? >> > > Yes, because you're setting [dihedrals] as if they were restraints. > Dihedrals have a multiplicity, phase angle (not the angle you want it to > be, it's the shape and position of the minima in the function) and a force > constant. So mdrun is doing what you're telling it, but what you're telling > it doesn't make physical sense. > > [ intermolecular_interactions ] >> [ bonds ] >> ; ai aj type bA kA bB kB >> 1391 2615 6 0.654 0.0 0.654 4184.0 >> >> [ angles ] >> ; ai aj ak type thA fcA thB fcB >> 1393 1391 2615 1 88.8 0.0 88.8 41.84 >> 1391 2615 2614 1 32.9 0.0 32.9 41.84 >> >> [ dihedrals ] >> ; ai aj ak al type thA fcA thB fcB >> 1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84 >> 1393 1391 2615 2614 2 122.6 0.0 122.6 41.84 >> 1391 2615 2614 2610 2 12.8 0.0 12.8 41.84 >> >> >> Should I use the following [ dihedral_restraints ] part instead of the >> above [ dihedrals ] part? >> > > Yes, this would probably accomplish what you want. > > -Justin > > [ dihedral_restraints ] >> ; ai aj ak al type phiA dphiA fcA phiB dphiB >> fcB >> 1410 1393 1391 2615 1 -159.7 0.0 0.0 -159.7 0.0 >> 41.84 >> 1393 1391 2615 2614 1 122.6 0.0 0.0 122.6 0.0 >> 41.84 >> 1393 1391 2615 2614 1 12.8 0.0 0.0 12.8 0.0 >> 41.84 >> >> I think [ dihedral_restraints ] will be the same as [ dihedrals ] because >> the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are >> taken as 0 (zero), right? >> >> >> Thanks in advance >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Ahmet Yildirim -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
