[gmx-users] Question regarding rebuilding the simulation box

[ali.khourshaei71 at student.sharif.edu]

Dear Mark, 

Thanks for your response. Actually, my simulation box contains polarize
water + lipid. So, when I exert editconf on it, it consider the
particles of each water molecules ( wp p wm) as separate molecules and
then  when I want to do mdrun it gives me an error to revise my
system.top . But I know that this shouldn't happen. 

I used : 

editconf -f Input.gro -bt cubic  -o Input2.gro -p system.top 

At first in Input.gro: 

1041W        W 2449   2.572   2.578   7.383
1041W       WP 2449   2.632   2.668   7.473
1041W       WM 2449   2.702   2.738   7.573 

But, in Input2.gro : 

1041W        W 4273   2.572   2.578   7.383
1041W       WP 4274   2.632   2.668   7.473
1041W       WM 4275   2.702   2.738   7.573 

Sincerely, 

Ali