[gmx-users] dimensions of the box
RAHUL SURESH
drrahulsuresh at gmail.com
Mon Jan 8 12:18:47 CET 2018
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*
More information about the gromacs.org_gmx-users
mailing list