[gmx-users] dimensions of the box

[RAHUL SURESH]

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..

any suggestions?



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*