[gmx-users] Distance restraints exploding system
Trayder Thomas
trayder.thomas at monash.edu
Mon Sep 2 04:54:35 CEST 2013
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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