Sorry. The pymol and GROMACS give the same results for every three target dihedrals. The updated results are here: https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0
The results show that the average dihedrals are almost the same in both the state A and state B for both [dihedrals] or [dihedral_restraints]. I think this is normal? On 13 November 2017 at 09:49, Ahmet Yildirim <ahmedo...@gmail.com> wrote: > Hi, > > Let me take that in reverse order: >> >> Note that choosing appropriate atoms to apply restraints is not a trivial >> matter, and results can vary depending on the choices made. >> > I know. > > I doubt there's a bug. I tested this feature a lot myself and have used >> it. How different are the dihedrals in the B-state vs. the A-state, and how >> much do they differ from the target values? >> > > The dihedrals are almost the same in both the state A and state B (except > for the first one) when the [dihedrals] or [dihedral_restraints] is used. > Please see the results https://www.dropbox.com/s/rdw6 > lg0c4xviufk/dih.pdf?dl=0 > > I think there is bug? > > On the other hand, the pymol and GROMACS calculate differently the first > target dihedral angle between 1587, 1581, 1579 and 14 atoms, respectively > -155 and 66. I don't know why? That is strange? Note that I used -155 > degrees obtained from pymol as a target value of the first dihedral in the > simulation. The other two target dihedrals are the same for both pymol and > GROMACS. > > Thanks. > > On 13 November 2017 at 01:55, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 11/10/17 11:59 PM, Ahmet Yildirim wrote: >> >>> 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? >>> >> >> I doubt there's a bug. I tested this feature a lot myself and have used >> it. How different are the dihedrals in the B-state vs. the A-state, and how >> much do they differ from the target values? Note that choosing appropriate >> atoms to apply restraints is not a trivial matter, and results can vary >> depending on the choices made. >> >> -Justin >> >> 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 >>>>> <https://maps.google.com/?q=the+eq.+4.84+in+the+manual+will+be+equal&entry=gmail&source=g>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. >>>> >>>> >>> >>> >> -- >> ================================================== >> >> 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 > -- 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? 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