[gmx-users] distance restraints fails

[Mark Abraham]

On 13/04/2012 3:08 AM, Qinghua Liao wrote:
> Dear gmx users,
>
> I tried to apply distance restraints to my system, but I found that it 
> failed because the distance between the restraints atoms in the last 
> frame is bigger than what we want.

Distance restraints aren't magic. There has to be an accessible 
simulation path from your initial conditions to one that satisfies the 
restraints. So far you haven't found one - there need not be one.

Mark

> Here are the parameters for distance restraints in the topology file:
>
> [ distance_restraints ]
> ; ai   aj type index type' low   up1   up2  fac
>     8  192  1   0   1   0.0   0.3   0.4   2.5
>   18  203  1   0   1   0.0   0.3   0.4   2.5
>   20  205  1   0   1   0.0   0.3   0.4   2.5
>
> and also I tried this (added four other distance restraints in the 
> same two groups):
> [ distance_restraints ]
> ; ai   aj type index type' low   up1   up2  fac
>    7  193  1   0   1   0.0   0.3   0.4   2.5
>    8  192  1   0   1   0.0   0.3   0.4   2.5
>   11  195  1   0   1   0.0   0.3   0.4   2.5
>   18  202  1   0   1   0.0   0.3   0.4   2.5
>   20  202  1   0   1   0.0   0.3   0.4   2.5
>   18  203  1   0   1   0.0   0.3   0.4   2.5
>   20  205  1   0   1   0.0   0.3   0.4   2.5
>
> I am sure that the atom numbers are right.
> And the following lines are the mdp file I used:
>
> title               =  PDXN  of Abeta in H2O
> ;cpp                 =  /lib/cpp   ; prepocessor of the current machine
> define              = ;-DPOSRES
> integrator          =  md       ; molecular dynamics algorithm
> tinit               =  0.0      ; start time and timestep in ps
> dt                  =  0.002    ; time step in ps
> nsteps              =  1000000   ; number of steps for 1000 ns run
> emtol               =  100    ; convergence criterion
> emstep              =  0.05      ; intial step size
> nstlist             =  0       ; step frequency for updating neighbour 
> list
> ns_type             =  simple ;grid     ; method for neighbour 
> searching (?)
> nstxout             =  5000     ; frequency for writing coords to 
> output .trr file
> nstvout             =  0     ; frequency for writing velocities to 
> output...should be same as nstxout
> nstfout             =  0        ; frequency for writing forces to output
> nstlog              =  5000      ; frequency for writing energies to 
> log file
> nstenergy           =  5000      ; frequency for writing energies to 
> energy file
> nstxtcout           =  5000     ; frequency for writing coords to xtc traj
> xtc_grps            =  system   ; group(s) whose coords are to be 
> written in xtc traj
> energygrps          =  system   ; group(s) whose energy is to be 
> written in energy file
>
> ;distance restraints
> disre               = simple
> disre_fc            = 20000 ; for the force, I tried 3000, 6000, 10000 
> and 15000, but all the tests failed
> disre_mixed         = yes
> disre_weighting     = equal
> disre_tau           = 10
> nstdisreout         = 100
> ;
> comm_mode           = angular
> nstcomm             = 10
> comm_grps           = system
> ;
> pbc                 =  no       ;xyz      ; use pbc
> rlist               =  0 ;1.4      ; cutoff lengths (nm)
> epsilon_r           =  1.0      ; Dielectric constant (DC) for 
> twin-range or DC of reaction field
> niter               =  100      ; Some thingies for future use
> fourierspacing   =  0.16
> fourier_nx          =  30
> fourier_ny          =  30
> fourier_nz          =  30
> coulombtype         =  Cut-off      ; truncation for minimisation, 
> with large cutoff
> rcoulomb            =  0 ;1.4
> rcoulomb-switch     =  0
> vdw-type                 = Cut-off  ; truncation for minimisation, 
> with large cutoff
> rvdw-switch              = 0
> rvdw                     = 0 ; 1.4   ; cut-off lengths
> ;pme_order                = 6    ; EWALD/PME/PPPM parameters
> ;ewald_rtol               = 1e-05
> ;ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = yes
>  Free energy control stuff
> free_energy              = yes
> init_lambda              = 0.0
> delta_lambda             = 0
> sc_alpha                 =0.5
> sc-power                 =1.0
> sc-sigma                 = 0.3
> ;nstcomm             =  0        ; number of steps for centre of mass 
> motion removal (in vacuo only!)
> Tcoupl              =  V-rescale  ;Berendsen
> tc_grps             = system     ;Other Water_and_ions
> tau_t               = 0.5   ; 0.5
> ref_t               = 300   ;   300
> Pcoupl              =  no
> ;Pcoupltype          =  Isotropic
> ;tau_p               =  1.0  1.0 1.0
> ;ref_p               =  1.0  1.0 1.0
> ;compressibility     =  4.5e-5   ; compressibility
> annealing           =  no       ; SIMULATED ANNEALING CONTROL
> ;zero_temp_time      =  0        ; Time at which temperature should be 
> zero (ps)
> gen_vel             =  yes
> gen_temp            =  300
> gen_seed            =  -1
> constraints         =  all-bonds  ; OPTIONS FOR BOND CONSTRAINTS
> constraint-algorithm  = Lincs   ; Type of constraint algorithm
> lincs_order         =  4        ; Highest order in the expansion of 
> the constraint coupling matrix
> lincs_warnangle     =  30       ; Lincs will write a warning to the 
> stderr if in one step a bond rotates
>                                 ; over more degrees than
> unconstrained-start      = no   ; Do not constrain the start configuration
> ;Shake-SOR                = no   ; Use successive overrelaxation to 
> reduce the number of shake iterations
> ;shake-tol                = 1e-04 ; Relative tolerance of shake
> morse                    = no   ; Convert harmonic bonds to morse 
> potentials
>
>
> Could someone help me to figure it out? Is there some parameter that I 
> missed to add? Thanks very much~
>
> -- 
> Best Regards,
>
> Qinghua
>
>
>
>

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