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 [ intemolecular_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? 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.