[gmx-users] Changes in the simulation box after the production run
Dallas Warren
dallas.warren at monash.edu
Mon Sep 18 01:30:52 CEST 2017
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
>>>>>
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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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