[gmx-users] constraining multiple types of bonds

[Justin Lemkul]

On 11/8/12 1:07 PM, tarak karmakar wrote:
> Dear All,
>
>
> In my system I need to fix three types of bonds
>
> 1) Metal-Ligand distance at a particular value given in PDB ( not covalent)

These require a merged [moleculetype] and are best implemented using simple 
harmonic interactions (bond type 6) or distance restraints.

> 2) I need to fix some of the bond lengths (covalent) for the substrate molecule.

Some, but not all?  That doesn't make sense to me.

> 3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.)
>

These are created using the .mdp settings shown below.

-Justin

>
> My input .mdp file is given below
>
> ; 7.3.3 Run Control
> integrator              = md-vv                 ; md integrator
> tinit                   = 0                         ; [ps] starting time for run
> dt                      = 0.001                 ; [ps] time step for integration
> nsteps                  = 5000000               ; maximum number of
> steps to integrate, 0.001 * 20,00,000 = 2 ns
> 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                 = 5000                 ; [steps] freq to write
> coordinates to trajectory
> nstvout                 = 5000                 ; [steps] freq to write
> velocities to trajectory
> nstfout                 = 5000                 ; [steps] freq to write
> forces to trajectory
> nstlog                  = 1000                 ; [steps] freq to write
> energies to log file
> nstenergy               = 1000                 ; [steps] freq to write
> energies to energy file
> nstxtcout               = 1000                 ; [steps] freq to write
> coordinates to xtc trajectory
> xtc_precision           = 1000                 ; [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                   = 1.2                   ; [nm] cut-off
> distance for the short-range neighbor list
>
> nsttcouple              = 1
> nstpcouple              = 1
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME                   ; Particle-Mesh Ewald
> electrostatics
> rcoulomb                = 1.2                   ; [nm] distance for
> Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype                 = cut-off               ; twin-range cut-off
> with rlist where rvdw >= rlist
> rvdw                    = 1.2                   ; [nm] distance for LJ cut-off
> DispCorr                = EnerPres              ; apply long range
> dispersion corrections for energy
>
> ; 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                  = Nose-Hoover                   ; Nose-Hoover
> temperature coupling
> tc_grps                 = Protein    Non-Protein        ; groups to
> couple seperately to temperature bath
> tau_t                   = 1.0        1.0                ; [ps] time
> constant for coupling
> ref_t                   = 300        300                ; [K]
> reference temperature for coupling
>
> ; 7.3.15 Pressure Coupling
> pcoupl                  = MTTK                          ; pressure
> coupling where box vectors are variable
> pcoupltype              = isotropic                     ; pressure
> coupling in x-y-z directions
> tau_p                   = 1.0                           ; [ps] time
> constant for coupling
> compressibility         = 4.5e-5                        ; [bar^-1]
> compressibility
> ref_p                   = 1.0                           ; [bar]
> reference pressure for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel                 = no                            ; velocity
> generation turned off
>
> ; 7.3.18 Bonds
> constraints             = h-bonds
> constraint_algorithm    = SHAKE                         ; SHAKE
> Constraint Solver
> shake_tol               = 1.0e-5
>
>
>
>
> So I'm bit confused how to implement constraints algorithm for these
> type of problem. If I do use the above set up then it is showing
> following error
>
> Program mdrun, VERSION 4.5.5
> Source code file: invblock.c, line: 79
>
> Fatal error:
> Double entries in block structure. Item 5247 is in blocks 1371 and 1370
>   Cannot make an unambiguous inverse block.
>
>
> Thanks
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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