[gmx-users] how to set pull code in gmx 4

Li Yang liyang1980_0_0 at 163.com
Mon Oct 20 17:27:38 CEST 2008

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

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