[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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