[gmx-users] pulldim vectors in pull code

Mauricio Sica msica at unq.edu.ar
Tue Oct 31 21:21:57 CET 2006

Dear users

I have the following problem. I'm using the pull code to bring near two
peptides initially 2.7 nm apart. The problem is that the run crush when I
choose "pulldim = Y Y Y or Y N N ", but doesn't when I use N N Y. I can't
understand what's wrong.
Maybe I don't understand what's the vector I am choosing in pulldim option.
I know it is the x, y or z axis. But is it a box vector? A distance vector?
In this case, why x, y and z if distance is one-dimensional? It was not
clear (at least for me) in the manuals (3.2 or

Thanks in advance

My pull.ppa is
verbose = no
Skip steps = 10
runtype = constraint
ngroups = 1
group_1 =  G1
reference_group = GR
reftype = com_t0
reflag = 1
pulldim = Y Y Y or N N Y or Y N N ; the three options I used. Only N N Y
constraint_direction = 0.0 0.0 0.0
constraint_distance1 =
constraint_rate1 = -0.00007
constraint_tolerance = 0.1

Dr. Mauricio Pablo Sica
Laboratorio de Expresión y Plegado Proteico (LEPP)
Dpto. de Ciencia y Tecnología
Universidad Nacional de Quilmes (UNQ)
R. Saenz Peña 352 (B1876BXF)
Bernal, Pcia de Buenos Aires

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