[gmx-users] DNA-protein complex

[Marcelo Depólo]

2015-03-18 5:26 GMT-03:00 Urszula Uciechowska <
urszula.uciechowska at biotech.ug.edu.pl>:

>
> The force field that I used was ambe99bsc0, and my input file was:
> ; 7.3.3 Run Control
> integrator              = md                    ; md integrator
> tinit                   = 0                     ; [ps] starting time for
> run
> dt                      = 0.002                 ; [ps] time step for
> integration
> nsteps                  = 5000000               ; maximum number of steps
> to integrate, 0.002 * 2,500,000 = 5,000 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                 = 2500000       ; [steps] freq to write
> coordinates to trajectory
> nstvout                 = 2500000       ; [steps] freq to write velocities
> to trajectory
> nstfout                 = 2500000       ; [steps] freq to write forces to
>

Why such a low output frequency? You are writing every 5ns.. this is too
high for any kind of small system simulation.

> trajectory
> nstlog                  = 100           ; [steps] freq to write energies
> to log file
> nstenergy               = 500           ; [steps] freq to write energies
> to energy file
> nstxtcout               = 500           ; [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 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                  = v-rescale                     ; temperature
> coupling with Nose-Hoover ensemble
> 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                   = 310        310                ; [K] reference
> temperature for coupling
>
> ; 7.3.15 Pressure Coupling
> pcoupl                  = parrinello-rahman     ; pressure coupling where
> box vectors are variable
> pcoupltype              = isotropic             ; pressure coupling in
> x-y-z directions
> tau_p                   = 2.0                   ; [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             = all-bonds     ; convert all bonds to constraints
> constraint_algorithm    = LINCS         ; LINear Constraint Solver
> continuation            = yes           ; 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
>
>
It remains difficult to foresee anything without the protocol that you have
used. Just the production mdp file will not provide enough info to say
anything. Please send your protocol and mdp files.

Cheers!
-- 
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)