[gmx-users] Pull code

[Alex]

Hi all,

I have a group (DNA) I'd like to translate relative to the other group
(CNT) along the Z-direction so that DNA is the only group that's actually
moving.

The code I had prior to what I have now worked under GMX 4.5.something.
Since the syntax has changed in 5.0.x, I found Justin's old suggestions,
and this is what I have now:

;Pull code

pull                = umbrella

pull_geometry       = direction

pull_coord1_vec     = 0.0 0.0 1.0

pull_start          = yes

pull_coord1_init    = 0.0

pull_ngroups        = 2

pull_ncoords        = 1

pull_coord1_groups  = 1 2

pull_group1_name    = CNT

pull_group2_name    = DNA

pull_coord1_rate1   = 0.0002          ;nm per ps

pull_coord1_k       = 5000          ; kJ mol^-1 nm^-2

;end pull code


Does this look right? My simulation isn't nearly done, but I am looking at
the Z-displacement in pullx.xvg and it just oscillates around a single
value. The simulated time is now about 1.5 ns.


Thank you,


Alex