On Fri, Aug 30, 2013 at 8:56 AM, Trayder <trayder.tho...@monash.edu> wrote: > 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.
Not really. MD is chaotic. Small changes in initial conditions lead to different results. > If domain decomposition is the problem, then I would think disre-weighting = > equal shouldn't work either. > I'm stumped... anyone got any ideas? http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the usual suggestions - don't use P-R yet, try a smaller time step, make sure your system is close to the restrained regime (or be extra gentle until it is). Mark > 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 -- 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
