[gmx-users] Pull code
m21.tang at qut.edu.au
Thu Apr 23 01:17:49 CEST 2015
You can try constraint. In umbrella， both 2 groups move.
Sent from my Huawei Mobile
Alex <nedomacho at gmail.com> wrote:
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
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 = 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.
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