[gmx-users] Distance restraints exploding system

[Trayder]

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.
If domain decomposition is the problem, then I would think disre-weighting =
equal shouldn't work either.
I'm stumped... anyone got any ideas?

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.