[gmx-users] dimensions of the box

[RAHUL SURESH]

Thank you all

On Tue, 9 Jan 2018 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/8/18 6:18 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For a protein-ligand simulation,
> >
> > for the command
> >
> > gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0 -c
> >
> > Read 680 atoms
> > Volume: 25.6402 nm^3, corresponds to roughly 11500 electrons
> > No velocities found
> >      system size :  3.411 17.359  3.004 (nm)
> >      diameter    : 17.543               (nm)
> >      center      :  5.138 15.619  2.935 (nm)
> >      box vectors :  3.411  2.687  2.798 (nm)
> >      box angles  :  90.00  90.00  90.00 (degrees)
> >      box volume  :  25.64               (nm^3)
> >      shift       :  4.633 -5.847  6.837 (nm)
> > new center      :  9.771  9.771  9.771 (nm)
> > new box vectors : 19.543 19.543 19.543 (nm)
> > new box angles  :  90.00  90.00  90.00 (degrees)
> > new box volume  :7463.88               (nm^3)
> >
> > System size looks so large, which eventually consume more computational
> > time. For 100ps nvt/npt it takes around 6 hours, which normally gets done
> > in 3-5 mins..
>
> Sounds like you're comparing apples and oranges and hoping for the same
> result; just because system X runs at a given speed doesn't mean system
> Y will. You have a system here that is extended along the y-axis,
> requiring a huge box. That's inherently going to run pretty slow, since
> the box is cubic and about an order of magnitude larger in each
> dimension than an "average" system.
>
> -Justin
>
> --
> ==================================================
>
> 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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*