[gmx-users] Distance restraints exploding system
Rafael I. Silverman y de la Vega
rsilverm at ucsc.edu
Mon Sep 2 21:32:15 CEST 2013
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 <trayder.thomas at monash.edu>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 <mark.j.abraham at gmail.com
> >wrote:
>
> > On Fri, Aug 30, 2013 at 8:56 AM, Trayder <trayder.thomas at 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.
> > > --
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