[gmx-users] Steered MD: Gromacs 4.0

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Mar 11 00:16:27 CET 2010

Dear Matt:

pull_vec1                 = -31.07-15.37 9.89
is not equal to
pull_vec1                 = -31.07 -15.37 9.89

There could be other problems, but I would start there.

-- original message --


I am having some trouble using the COM pulling code (Gromacs 4.0). I  
will try to describe the problem as
best I can and hopefully someone will be able to point me in the right  

Basically what I would like to do is pull a ligand (LIG) along a specified
path from the interior of a protein to the exterior (Steered MD simulation).
Using the following .mdp file I was able to pull the ligand, but it  
did not travel
along the path that I thought it would (ie along the vector specified  
in pull_vec1).

Pull section of my md.mdp file:

pull                        = umbrella
pull_geometry                 = position
pull_dim                 = Y Y Y

pull_r1                 = 1
pull_r0                 = 1.5
pull_constr_tol                = 1e-06
pull_start                 = no
pull_nstxout                 = 10
pull_nstfout                 = 1
pull_ngroups                 = 1

pull_group0                 =
pull_weights0                 =
pull_pbcatom0                 = 0
pull_group1                 = LIG
pull_weights1                 =
pull_pbcatom1                 = 0
pull_vec1                 = -31.07-15.37 9.89
pull_init1                 = 43.416 66.914 40.125
pull_rate1                 = 0.001
pull_k1                 = 500
pull_kB1                =

I specified pull_vec1 as the vector I would like to pull the ligand  
along (ie -x,-y,+z).
Looking at the simulation in VMD the ligand traveled in the (+x, +y,  
+z) direction.

In this trial I specified pull_init1 as the point I would like the  
spring to be attached to the ligand.

I have read the gromacs 4.0 manual and many of the posts online, but I  
still cannot seem to figure out what values are required in the  
parameter file.
I know the following pieces of information, but I don't know how/if  
they fit into the parameter file:

1. The point where I would like the spring to be attached to the ligand
2. The vector along which I would like the ligand to travel
3. The distance between a reference atom in the protein and the  
desired spring attachment point on the ligand

Anyone have any ideas of what i am missing or doing wrong?  Or if I am  
missing some fundamental concept here?

Matt Danielson

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