[gmx-users] dimensions of the box

[Justin Lemkul]

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

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