[gmx-users] Pulling simulation of the unfolding of a protein

[Lalita Shaki]

Dear gromacs users,

I want to perform a pulling simulation of the unfolding of a protein
but I am not sure which pull_geometry is the correct one for this
problem. First I try using position with pull-dim= Y Y Y, since It
will allow the force to have components in the three dimensions, even
is the pull_vector is oriented only in one. The problem of this setup
is that I need a really large box, at leat all the dimensions should
be twice the lenght of my protein, since the pulling code checks that
the distance between the pulll and reference group is smaller than
0.49 the large of all the dimension. If I choose pull_geometry=
direction I have the same problem.

A possible solution will be to use pull-geometry= position and
pull-dim= N N Y, but this will imply that I dont allow the force to
have components in the other two dimension, which is unrealistic.

Is there a setup which I can used that allows the force to have
component in the three dimension and at the same time to use a box
that it is only large in the pulling direction?

Thank you

Lalita

-- 
Lalita S. Uribe.
European Master in Theoretical Chemistry and Computational Modeling.
PhD student. Johannes Gutenberg-Universität Mainz