[gmx-users] Distance restraints exploding system

[Mark Abraham]

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.
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists