[gmx-users] Changes in the simulation box after the production run
Justin Lemkul
jalemkul at vt.edu
Mon Sep 18 01:00:15 CEST 2017
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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--
==================================================
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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