Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions.
I'm attempting to use: ; Restraints disre = simple disre-weighting = conservative disre-fc = 1000 It blows up within 100 steps unless: I run on a single core (+gpu) or disre-fc = <100 or disre-weighting = equal If disre-weighting = conservative is causing extreme forces, then I figure it should do the same on 1 core. If domain decomposition is the problem, then I would think disre-weighting = equal shouldn't work either. I'm stumped... anyone got any ideas? Thanks in advance, -Trayder Distance restraints excerpt: ; ai aj type index type’ low up1 up2 fac ; 2 symmetric hydrogens 1306 1389 1 10 1 0.0 0.548 1.0 1.0 1306 1396 1 10 1 0.0 0.548 1.0 1.0 ; Diastereotopic methyl groups 1306 1374 1 11 1 0.0 0.654 1.0 1.0 1306 1375 1 11 1 0.0 0.654 1.0 1.0 1306 1376 1 11 1 0.0 0.654 1.0 1.0 1306 1385 1 11 1 0.0 0.654 1.0 1.0 1306 1386 1 11 1 0.0 0.654 1.0 1.0 1306 1387 1 11 1 0.0 0.654 1.0 1.0 Full mdp: ; Run Control integrator = md ; simulation algorithm tinit = 0 dt = 0.002 nsteps = 500000 ; ; Output Control nstxout = 200000 ; write coordinates to .trr nstvout = 200000 ; write velocities to .trr nstlog = 1000 ; write energies to .log nstenergy = 4000 ; write energies to .edr nstxtcout = 1000 ; write coordinates to .xtc ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb = 0.9 ; cut-off distance for coulomb epsilon_r = 1 ; dielectric constant rvdw = 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4 ; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr = EnerPres ; long range dispersion corrections ; ; Restraints disre = simple disre-weighting = conservative disre-fc = 1000 ; ; Temperature Coupling Tcoupl = v-rescale ; type of temperature coupling tc-grps = Protein non-Protein ; coupled groups tau_t = .1 .1 ; T-coupling time constant (ps) ref_t = 310 310 ; reference temperature (K) ; ; Pressure Coupling Pcoupl = parrinello-rahman ; type of pressure coupling Pcoupltype = isotropic ; pressure coupling geometry tau_p = 2.0 ; p-coupling time constant (ps) compressibility = 4.5e-5 ; compressibiity ref_p = 1.0 ; reference pressure (bar) ; ; Velocity Generation gen_vel = no ; generate initial velocities ; ; Bonds constraints = all-bonds ; which bonds to contrain constraint_algorithm = lincs ; algorithm to use lincs_order = 4 lincs_iter = 2 -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-exploding-system-tp5010842.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
