Hi again, one more piece of info. If I move the subset of restraints that are intra-protein into a separate [ distance_restraints ] section just after inclusion of the ligand topology and run that , the dist.rest energies and violation start appearing in the log file - so the dist. rest. section itself seems to be ok.
Still the dist. restraints in the [ intermolecular_interactions ] appear to be ignored However gmx disre now complains that all parameters should be consecutive Error message: Source file: src/gromacs/listed-forces/disre.cpp (line 174) Function: init_disres(FILE*, const gmx_mtop_t*, t_inputrec*, const t_commrec*, const gmx_multisim_t*, t_fcdata*, t_state*, gmx_bool)::__lambda0 Assertion failed: Condition: type_max - type_min + 1 == dd->nres All distance restraint parameter entries in the topology should be consecutive any help appreciated! best, Eiso E On Mon, May 13, 2019 at 2:49 PM Eiso AB <eis...@gmail.com> wrote: > Hi, > I've setup an mdrun with [ distance restraints ] but the restraints don't > seem to have any effect on the simulation, so I'm wondering if there's > anything i need to do to switch them on that I missed. > > gmx disre or gmx nmr doesn't give any info about restraints. > and the .log file doesn't show any energy component for Distance > Restraints, e.g. > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih. > 4.14550e+03 1.13252e+04 1.29502e+04 9.20032e+01 6.00131e+02 > LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. > 5.01723e+03 6.08476e+04 3.13964e+05 -2.12124e+06 5.15532e+03 > Potential Kinetic En. Total Energy Conserved En. Temperature > -1.70714e+06 2.85181e+05 -1.42196e+06 -1.34064e+06 2.99828e+02 > Pressure (bar) Constr. rmsd > 1.15517e+02 4.10744e-06 > > I have defined restraints between protein, ligand and a few waters - all > in different [molecules] > - so I used [ intermolecular_interactions ] followed by [ > distance_restraints ] > > > my topol.top ends like this : > > [ system ] > ; Name > Protein in water > > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > lig 1 > SOL 35926 > NA 4 > > [ intermolecular_interactions ] > > [ distance_restraints ] > ; ai aj type index type' low up1 up2 fac ; # source > 465 564 1 0 1 0.2540 0.2540 0.4115 1 ; # 308 ile hd+ 216 val > hg1+ 2.54 > 465 565 1 0 1 0.2540 0.2540 0.4115 1 ; # > 465 566 1 0 1 0.2540 0.2540 0.4115 1 ; # > 466 564 1 0 1 0.2540 0.2540 0.4115 1 ; # > 466 565 1 0 1 0.2540 0.2540 0.4115 1 ; # > 466 566 1 0 1 0.2540 0.2540 0.4115 1 ; # > 467 564 1 0 1 0.2540 0.2540 0.4115 1 ; # > 467 565 1 0 1 0.2540 0.2540 0.4115 1 ; # > 467 566 1 0 1 0.2540 0.2540 0.4115 1 ; # > [...snap...] > 1607 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # 170 leu hd1# 411 lig h09 > 5.68 > 1608 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # > 1609 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # > [ ..snap ... ] > 2720 5571 1 52 2 0.1900 0.1900 0.2900 1 ; # 217 asp od1 501 sol hw2 > 1.90 > 2720 5569 1 53 2 0.3000 0.3000 0.4000 1 ; # 217 asp od1 501 sol ow > 3.00 > > > disre is set to simple. From the mdout.mdp > > []$ grep disre mdout.mdp > > ; Distance restraints type: No, Simple or Ensemble > disre = Simple > ; Force weighting of pairs in one distance restraint: Conservative or Equal > disre-weighting = Conservative > ; Use sqrt of the time averaged times the instantaneous violation > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > ; Output frequency for pair distances to energy file > nstdisreout = 100 > > > gmx dump shows that the run topology has the distance restraints and looks > ok to me > > gmx dump -s md_0_10.tpr |grep -10 dis > > [..snap..] > Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision) > Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision) > disre = Simple > disre-weighting = Conservative > disre-mixed = false > nstdisreout = 100 > 0 type=1038 (DISRES) 464 563 > 1 type=1038 (DISRES) 464 564 > 2 type=1038 (DISRES) 464 565 > 3 type=1038 (DISRES) 465 563 > 4 type=1038 (DISRES) 465 564 > 5 type=1038 (DISRES) 465 565 > [..snap ...] > D.R.Viol. (nm): > nr: 0 > [...snap...] > > functype[1038]=DISRES, label= 0, type=1, low= 2.54000008e-01, > up1= 2.54000008e-01, up2= 4.11500007e-01, fac= 1.00000000e+00) > functype[1039]=DISRES, label= 1, type=1, low= 2.56999999e-01, > up1= 2.56999999e-01, up2= 4.12600011e-01, fac= 1.00000000e+00) > functype[1040]=DISRES, label= 2, type=1, low= 3.72999996e-01, > up1= 3.72999996e-01, up2= 4.80199993e-01, fac= 1.00000000e+00) > functype[1041]=DISRES, label= 3, type=1, low= 3.84000003e-01, > up1= 3.84000003e-01, up2= 4.88200009e-01, fac= 1.00000000e+00) > functype[1042]=DISRES, label= 4, type=1, low= 2.33999997e-01, > up1= 2.33999997e-01, up2= 4.04900014e-01, fac= 1.00000000e+00) > functype[1043]=DISRES, label= 5, type=1, low= 2.39999995e-01, > up1= 2.39999995e-01, up2= 4.06699985e-01, fac= 1.00000000e+00) > functype[1044]=DISRES, label= 6, type=1, low= 3.03000003e-01, > up1= 3.03000003e-01, up2= 4.35000002e-01, fac= 1.00000000e+00) > > etc... > > Any suggestions about what is wrong here would be appreciated > Thanks, > > Eiso > > > > > -- 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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