[gmx-users] Changes in the simulation box after the production run
Mahsa E
ebadi.mahsa at gmail.com
Mon Sep 18 10:30:51 CEST 2017
Thank you very much for the links!
Best regards,
Mahsa
On Mon, Sep 18, 2017 at 1:30 AM, Dallas Warren <dallas.warren at monash.edu>
wrote:
> These two images will help you see what is going on:
>
> https://twitter.com/dr_dbw/status/909559339366572032 - shows a
> molecule that appears to be outside the box.
>
> https://twitter.com/dr_dbw/status/909559783291723776 - however, that
> molecule actually enters through the opposite face of the box.
> 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 09:22, Mahsa E <ebadi.mahsa at gmail.com> wrote:
> > 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
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
> >>>>> * Please search the archive at http://www.gromacs.org/
> >>>>>
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> >>>>
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> or
> >>>>>
> >>>> send a mail to gmx-users-request at gromacs.org.
> >>>> --
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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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
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