[gmx-users] pull code

[David L. Bostick]

Hello all,

I want to measure the pmf of an ion traversion across a membrane protein.
I haven't decided whether I want to use umbrella sampling or constraint
force measurement but I'm playing with the pull code for both.  However, I
want to constrain/restrain (constraint force sampling / umbrella sampling)
the ion with respect to the protein backbone in the z dimension only.  Is
this possible with the input.ppa options?  Does setting 

direction = 0.0 0.0 1.0 

do this?

So far, I have tried to measure constraint force with the following options
in the .ppa file:

verbose                  = no
runtype                  = constraint
group_1                  = CL
reference_group          = Backbone
reftype                  = com
reflag                   = 1
direction                = 0.0 0.0 1.0

but I get Not a Number for my output forces.

I have also tried umbrella sampling for one point using:

verbose                  = no
runtype                  = umbrella
group_1                  = CL
reference_group          = Backbone
reftype                  = com
reflag                   = 1
direction                = 0.0 0.0 1.0
width                    = 1000.0

but I get an output file with one set of 3D coordinates (of the group_1 I
suppose) and another set of coordinates on the right side of the file ..
all reading 0.0 0.0 0.0.

Can anyone offer any help?

David 

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-