On 6/17/12 7:47 AM, Eudes Fileti wrote:
Hello guys, I have tried to calculate the PMF for a dimer in a
rectangular box of dimensions 3 x 3 x 7. However, the simulation
stops when the COM separation is above 1.49 (ie half
of the smallest dimension of the box. Since I am pulling along
the Z axis at a distance that would be up to 3.5 nm.
I've tried both pull_geometry, distance and direction, to try to get
around this, but I have not been successful.
Do I have to use the dimensions of the box as twice the COM
distance (in my case: 5 x 5 x 5; to give me r_max = 2.5nm)?
Some of you could give me a hand?
DIRECTION
pull = umbrella
pull_geometry = direction
pull_dim = Y Y Y
pull_group0 = mol_0
pull_group1 = mol_1
pull_rate1 = 0.01
pull_vec1 = 0.0 0.0 1.0
pull_k1 = 3000
DISTANCE
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_group0 = mol_0
pull_group1 = mol_1
pull_rate1 = 0.01
pull_vec1 = 0.0 0.0 0.0
pull_k1 = 3000
If you only want to pull along the z-axis using the "distance" geometry, then
you should not set "Y Y Y" for the pull_dim here; that will cause pulling along
all 3 axes, hence why you're having problems in x and y. For z-only, set "N N Y."
It is not clear to me why the settings for the "direction" pulling do not work.
In that case, the settings for pull_dim are ignored and pull_vec1 is used.
There is a different setting that should be more appropriate. Read in the
manual about the "direction_periodic" geometry. It overcomes these issues.
Otherwise, your box needs to be at least twice the COM distance at all times.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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