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 --
Hi,
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
direction!
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?
Thanks,
Matt Danielson
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