Specific colvar component needed.

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

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

Any suggestion is truly valuated.
Thanks in advance.

German Miño Galaz.
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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