To wrap this up for anyone who stumbles across this in the future: The 'solution' I ended up going with was to avoid using hydrogen atoms in the restraints, instead restraining to the e.g. methyl carbon and adding a fudge factor to the restraint length to account for the C-H distance. This results in slightly 'looser' restraints but actually runs stably.
-Trayder On Tue, Sep 3, 2013 at 5:32 AM, Rafael I. Silverman y de la Vega < [email protected]> wrote: > Have you tried with even less restraints? I found systems are not always > stable with more than the bare minimum of restraints > > > On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas <[email protected] > >wrote: > > > It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to > have > > an impact. I've tried being gentle, slowly turning up the force constant > > and running for 1 ns for each value but as soon as the force constant > > approaches 100 it crashes. > > The starting structure was generated with the same restraints, so it is > > very close. I have tried using slightly different starting structures as > > well. > > > > I've tried running it with only 3 restraints (1 methyl group to 1 > hydrogen > > with the restraints extended by 0.2nm so that all hydrogens are within > the > > restraint distance) and I'm getting a segmentation fault (no LINCS > > warnings) at 100 steps. It runs fine with any combination of 2 hydrogens > > restrained, but as soon as I restrain the 3rd one I get a segmentation > > fault (this occurs with either setting for disre-weighting). So it seems > to > > fair better with more restraints? > > > > The more I try to solve this problem the less it makes sense! > > > > -Trayder > > > > > > On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham <[email protected] > > >wrote: > > > > > On Fri, Aug 30, 2013 at 8:56 AM, Trayder <[email protected]> > > > 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 [email protected] > > > > 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. 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