[gmx-users] DPOSRE not restraining

[Justin Lemkul]

On 7/28/12 1:49 PM, tarak karmakar wrote:
> Dear All ,
>
>      I wanted to keep all the molecules other than water fixed [
> positiion restraints]. So for that I have performed short NVT
> [simulation with DEPOSRE] after minimization, but while seeing the
> movie of the trajectory in VMD I see the protein backbone is moving.
>      So did I miss something prior to the simulation. The nvt.mdp file
> is given below
>

Well -DEPOSRE is going to act differently than -DPOSRES.  Check what your 
topology expects.  For a .top written by pdb2gmx, -DPOSRES is correct based on 
the default #include statement.  Check carefully for typos or any incorrect 
modifications you have made for the topology.

-Justin

> ; 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                      = 0.0005              ; [ps] time step for integration
> nsteps                  = 400000              ; maximum number of
> steps to integrate, 0.0005 * 40,000 = 2 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                 = 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                  = 5000           ; [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                   = 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             = all-bonds     ; constraining all 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
>

-- 
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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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