[gmx-users] Pull code

[Alex]

Well, no, i don't want two. I want one! :)

On Wed, Apr 22, 2015 at 5:17 PM, Ming Tang <m21.tang at qut.edu.au> wrote:

> Hi，Alex
>
> You can try constraint. In umbrella， both 2 groups move.
>
> Sent from my Huawei Mobile
>
> Alex <nedomacho at gmail.com> wrote:
>
> 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
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