[gmx-users] Problems with pulling code

Marisa Roman mbr35 at drexel.edu
Tue Mar 10 21:01:51 CET 2009

Hi there,
I used the old Gromacs 3.3 for pulling simulations using afm with success. 
For the new upgrade, I cannot understand the new configuration for the former standard afm constant velocity pulling with one reference group and the pulling group.
For example, when the manual says
      Pull to the position of the reference group plus pull init + time*pull rate*pull vec.

Where is it pulling? How is that it pulls to the position of the reference group? Wa
I have searched the archives for more details of the new convention for pulling simulations but not enough.

Here is my pulling code for the .mdp file.
pull_geometry = position
pull_group0 = a_5    ;the C-alpha
pull_group1 = a_757   ;the N-terminal
pull_dim = N N Y       ;pulling in the Z-direction
pull_k1 = 500          ;spring constant?
pull_rate1 = 0.05       ;velocity
pull_vec1 = 0.0 0.0 1.0  ;direction of the pulling
pull_init1 = 1.46  1.19  3.05 ;pulling from the N-terminal, positions respect to the reference group
pull_nstxout = 1000
pull_nstfout = 1000

Any comments will be more than welcome

Marisa Roman
mbr35 at drexel.edu
Physics Dept. 
Drexel University - Philadelphia - USA

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