[gmx-users] how to set pull code in gmx 4
gmx3 at hotmail.com
Mon Oct 20 19:23:57 CEST 2008
> Date: Mon, 20 Oct 2008 23:27:38 +0800
> From: liyang1980_0_0 at 163.com
> To: gmx-users at gromacs.org
> Subject: RE: RE: [gmx-users] how to set pull code in gmx 4
> Hi Berk
> Thanks for your reply
> > If you use pull_geometry=distance you need to set the reference distance,
> > which would be (assuming you want 1 nm):
> > pull_init1 = 1
> Sorry for my poor expression.
> Take a example, In gmx 3.3, the pull dimension and position can be
> writen as:
> "pull_type = umbrella ; umbrella sampling
> pull_dim = N N Y ; pulling performed in Z dimension
> pos1 = 0 0 1" ; the reference distance in Z dimension is 1nm
> In gmx 4, for "pull_init1 = 1", which dimension of the reference
> distance does it mean ？
> Or say, there is still a single pulling performed in one dimension, like
> gmx 3.3, and when setting "pull_dim = N N Y", the "pull init1=1" means
> the reference distance in Z dimension is 1nm; while "pull_dim=Y N N"
> means the reference distance in X dimension is 1nm？
> Maybe my thinking sounds stupid, I don't know.
> Waiting for your reply.
> Li Yang
You chose pulling distance, so you pull along the distance vector between
groups 0 and 1. Since you choose pull_dim= N N Y, the distance is only
taken along Z. pull_init1=1 means a (starting) distance of 1.
So a distance of 1 nm in z. Note that group 1 could be 1 nm above OR below group 0.
Another (nearly indentical) setup would be:
pull_geometry = direction
pull_vec = 0 0 1
pull_init = 1
This would mean that group 1 is 1 nm above group 0.
In this case pull_dim is irrelevant, as long as z is Y.
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