Hi Dallas and other Gromacs users,
I used -pbc whole and -ur compact in the first step
"System" index group
And then, used the output file for -pbc cluster.
Choosing the "System" index for clustering gave the best result I got.
(Although there are still few lipids which are not completely in the
Hi Dallas,
Thanks for your reply.
I did try -pbc cluster for waters. It could fix it somehow but not
completely.
After that, I had to use -pbc center to fix it. Still, I do not get what I
want.
Unfortunately, some waters and lipids are appearing from the other side of
the box.
Cheers,
Mohsen
On
I have found the cluster option of -pbc to work well for putting
aggregates back together correctly. Some times you do need an index
file and appropriate groups to assist with it getting it right.
gmx trjconv -pbc cluster
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash
Dear Gromacs users,
I have an HII phase made of one inverted cylinder (and waters inside) in a
triclinic box with 90, 90, 60 angles. After running the simulation, this
cylinder become bent like a curve. I.e. is not a perfect cylinder anymore.
As a result, some water molecules and lipids pass the b
