From: Germán Andrés Miño (germino_at_u.uchile.cl)
Date: Mon May 07 2012 - 10:55:14 CDT
Hi namd2.8 users.
I would like to do and protein unfolding ABF calculation in an water
box with the following restrictions:
CA atom of the C-terminal fixed in space.
CA atom of the N-terminal moving along the (0,0,Z) axis.
I have tried with distanceZ (see below) component but my system drift
away from the Z axis.
I need to minimize the size of the water box (actually a rectangle)
because limitations in numbers of processors and computational time
available.
The colvar I am using now is:
colvarsTrajFrequency 2000
colvarsRestartFrequency 20000
colvar {
name d
width 0.1
lowerboundary 50.36
upperboundary 380.00
lowerwallconstant 10.0
upperwallconstant 10.0
distanceZ {
main { atomNumbers 1921
}
ref {
atomNumbers 959
}
axis (0.0, 0.0, 1.0)
}
}
abf {
colvars d
fullSamples 500
hideJacobian
}
Any suggestion is truly valuated.
Thanks in advance.
German Miño Galaz.
germino_at_u.uchile.cl
Postdoctoral Fellow of Grupo de Namomateriales (www.gnm.cl)
Departamento de Fisica
Universidad de Chile.
Palmeras 3425, Nunoa.
Santiago Chile
Tel: 0056-2-978-7439
Fax: 0056-2-2712973
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