[gmx-users] Pull code

[chris.neale at utoronto.ca]

In addition to what everyone else has said, please note that pull_dim  
= N N Y is going to allow X and Y distance components to get as  
large/small as they will without any restraint. This may be what you  
want, but if you want a distance, but want it to be mostly in Z, then  
pull_dim = Y Y Y and other parameters set appropriately.

Chris.

-- original message --

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Jun 30 18:27:47 CEST 2010

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Hi all

I am commencing the initial stages for he calculation of potential of
mean force of bringing together two cage molecules. I am following the
tutorial in such an exercise at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
In contrast to the tutorial I want to bring the two molecules together
along the z axis. I have generated an initial configuration in which the
COMs of the two molecules are 5.07 nm apart.
In the tutorial to separate a substrate from a protein you use the
following parameters in the mdp file.

; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = yes           ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Chain_B
pull_group1     = Chain_A
pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per n
pull_k1         = 1000          ; kJ mol^-1 nm^-


How should I alter this to pull the molecules together along the z axis?
I would've thought the following but I'm not too sure

pull        = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_rate1 = -0.01
pull_k1 = 1000


Obviously I have to play with the values, but it is the sign that I'm
interested in.

Many Thanks

Gavin