[gmx-users] Changes in the simulation box after the production run

[Dallas Warren]

Because that is how the system changed within the simulation time?

What exactly is the problem as you see it, and why do you think it is a problem?

And remember, you have a periodic boundary condition that means the
one edge of the box wraps around to the opposite one.  So "out of the
box" is a visualisation artefact, not a "problem".
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 18 September 2017 at 06:31, Mahsa E <ebadi.mahsa at gmail.com> wrote:
> Dear gmx-users,
>
> I did a 200 ns production md run in NVT ensemble for a simulation box of
> polymer chains. Before this step, I did the energy minimisation, NVT and
> NPT equilibration on the system. The problem is after the production run, I
> don't get the initial equilibrated packed box of polymer and it seems more
> like a circular shape with some parts of the chains out of the box. What is
> the reason for getting this result?
> For the MD run I used the mdp file below:
>
> ; 7.3.2 Preprocessing
>
> ;define                  =       ; defines to pass to the preprocessor
>
>
> ; 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                  = 100000000                ; maximum number of
> steps to integrate, 0.002 * 100000000 = 200000 ps
>
> comm_mode               = Linear                ; remove center of mass
> translation
>
> nstcomm                 = 100                     ; [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                 = 0         ; [steps] freq to write coordinates to
> trajectory
>
> nstvout                 = 0         ; [steps] freq to write velocities to
> trajectory
>
> nstfout                 = 0         ; [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
>
> cutoff-scheme            = verlet
>
> ; 7.3.9 Neighbor Searching
>
> nstlist                 = 20             ; [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                = 1.2           ; [nm] distance for Coulomb cut-off
>
>
> ; 7.3.11 VdW
>
> vdwtype                 = cut-off       ; twin-range cut-off with rlist
> where rvdw >= rlist
>
> vdw-modifier             = potential-switch
>
> rvdw-switch              = 1.1
>
> rvdw                    = 1.2           ; [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-6          ; relative strength of
> Ewald-shifted potential at rcoulomb
>
> ewald-rtol-lj            = 0.001
>
> lj-pme-comb-rule         = Geometric
>
> ewald-geometry           = 3d
>
> epsilon_surface          = 0
>
>
> ; 7.3.14 Temperature Coupling
>
> tcoupl                  = v-rescale                    ; temperature
> coupling with
>
> tc_grps                 = system        ; groups to couple seperately to
> temperature bath
>
> tau_t                   = 0.1                        ; [ps] time constant
> for coupling
>
> ref_t                   = 303                        ; [K] reference
> temperature for coupling
>
>
> ; 7.3.17 Velocity Generation
>
> gen_vel                 = no           ; generate velocities according to
> Maxwell distribution of temperature
>
> gen_temp                = 303           ; [K] temperature for Maxwell
> distribution
>
> gen_seed                = -1            ; [integer] used to initialize
> random generator for random velocities
>
>
> ; 7.3.18 Bonds
>
> constraints             = 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
>
> Best regards,
>
> Mahsa
> --
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