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

Mahsa E ebadi.mahsa at gmail.com
Mon Sep 18 01:23:16 CEST 2017


Thank you for you quick reply, Justin and Dallas! Very good point!

Best regards,
Mahsa





On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/17/17 6:57 PM, Mahsa E wrote:
>
>> Could you please see the link below for the input and output simulation
>> box:
>>
>> https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0
>>
>>
>> Actually, I thought since some of the chains went out of the simulation
>> box, then density have been changed. In my previous experience with
>> another
>> polymer, I didn't see this difference in the systems after the production
>> run, so I'm wondering if this is related to the stability of the system?
>>
>>
> As Dallas said, this is just a periodicity/visualization effect - there's
> no such thing as "outside" a periodic cell.
>
> Your "before MD" has "broken" molecules, i.e. all the atoms are visualized
> as being in the central image.  Your "after MD" is just those molecules
> made whole.  If you make the initial frame whole (trjconv -pbc whole), you
> will see a similar configuration.
>
> -Justin
>
>
> Best regards,
>> Mahsa
>>
>>
>>
>>
>>
>> On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren <dallas.warren at monash.edu
>> >
>> wrote:
>>
>> 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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>>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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