[gmx-users] Distance restraints exploding system
Trayder Thomas
trayder.thomas at monash.edu
Fri Sep 6 02:55:36 CEST 2013
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 <
rsilverm at ucsc.edu> 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 <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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