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 <mark.j.abra...@gmail.com>wrote: > 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 > -- 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
