[gmx-users] constraints algorithm

[Mark Abraham]

On 24/07/2012 2:37 PM, tarak karmakar wrote:
> Dear All,
>
>       In a protein simulation I imposed one bond constraint by
> incorporating the "[constraints]" block in topology file. On the other
> hand in .mdp file I have imposed constraints for the covalent hydrogen
> bonds by implementing the LINCS algorithm. After a short equilibration
> run I see the bond length is fixed [served my purpose], but then what
> algorithm it's making use of to constraint the specified bond ?

You told mdrun to use the LINCS algorithm for constraints. You created 
constraints in two different ways. It's all the same from there.

Mark

> The .mdp file is given below
>
> Thanks.
>
> ......................................................................................................................................................................................
> ; 7.3.2 Preprocessing
> ;define                  = -DPOSRES      ; defines to pass to the preprocessor
>
> ; 7.3.3 Run Control
> integrator              = md                    ; md integrator
> tinit                   = 0                     ; [ps] starting time for run
> dt                      = 0.001                ; [ps] time step for integration
> nsteps                  = 50000                ; maximum number of
> steps to integrate, 0.001 * 50,000 = 500 ps
> comm_mode               = Linear                ; remove center of
> mass translation
> nstcomm                 = 1                     ; [steps] frequency of
> mass motion removal
> comm_grps               = Protein Non-Protein   ; group(s) for center
> of mass motion removal
>
> ; 7.3.8 Output Control
> nstxout                 = 1000         ; [steps] freq to write
> coordinates to trajectory
> nstvout                 = 1000         ; [steps] freq to write
> velocities to trajectory
> nstfout                 = 1000         ; [steps] freq to write forces
> to trajectory
> nstlog                  = 100           ; [steps] freq to write
> energies to log file
> nstenergy               = 100           ; [steps] freq to write
> energies to energy file
> nstxtcout               = 100           ; [steps] freq to write
> coordinates to xtc trajectory
> xtc_precision           = 100           ; [real] precision to write
> xtc trajectory
> xtc_grps                = System        ; group(s) to write to xtc trajectory
> energygrps              = System        ; group(s) to write to energy file
>
> ; 7.3.9 Neighbor Searching
> nstlist                 = 1             ; [steps] freq to update neighbor list
> ns_type                 = grid          ; method of updating neighbor list
> pbc                     = xyz           ; periodic boundary conditions
> in all directions
> rlist                   = 0.8           ; [nm] cut-off distance for
> the short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
> rcoulomb                = 0.8           ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype                 = cut-off       ; twin-range cut-off with
> rlist where rvdw >= rlist
> rvdw                    = 0.8           ; [nm] distance for LJ cut-off
> DispCorr                = EnerPres      ; apply long range dispersion
> corrections
>
> ; 7.3.13 Ewald
> fourierspacing          = 0.12          ; [nm] grid spacing for FFT
> grid when using PME
> pme_order               = 4             ; interpolation order for PME, 4 = cubic
> ewald_rtol              = 1e-5          ; relative strength of
> Ewald-shifted potential at rcoulomb
>
> ; 7.3.14 Temperature Coupling
> tcoupl                  = Berendsen                     ; temperature coupling
> tc_grps                 = Protein    Non-Protein        ; groups to
> couple seperately to temperature bath
> tau_t                   = 0.1        0.1                ; [ps] time
> constant for coupling
> ref_t                   = 300        300                ; [K]
> reference temperature for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel                 = yes           ; generate velocities
> according to Maxwell distribution of temperature
> gen_temp                = 300           ; [K] temperature for Maxwell
> distribution
> gen_seed                = -1            ; [integer] used to initialize
> random generator for random velocities
>
> ; 7.3.18 Bonds
> constraints             = h-bonds       ; constraining covalent h-bonds
> constraint_algorithm    = LINCS         ; LINear Constraint Solver
> continuation            = no            ; no = apply constraints to
> the start configuration
> lincs_order             = 4             ; highest order in the
> expansion of the contraint coupling matrix
> lincs_iter              = 1             ; number of iterations to
> correct for rotational lengthening
> lincs_warnangle         = 30            ; [degrees] maximum angle that
> a bond can rotate before LINCS will complain
>
>