[gmx-users] COM Pulling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jan 21 16:03:28 CET 2010

Try changing

pull_dim = N N Y


pull_dim = Y Y Y

And check the manual for what it does.

Note that some of your other pull options are irrelevant tot he type  
of sampling that you appear to be doing, but that should not matter.


-- original message --

I have a results of my MD and i have found a water molecule that was getting
closer to my substrate on one frame of my dynamic. The distance is 3.4 A.
Now I have to immobillize this water on this distance during the next step
of MD by using a harmonic potential as the distance constraint, where the
force constant is about 200 kcal/....I understand that i have to create an
index file, it's ok, but my mdp is bad rather COM pulling in gromacs

protein - my substrate
LIN - my water


; Pull type: no, umbrella, constraint or constant_force

pull = umbrella

; Pull geometry: distance, direction, cylinder or position

pull_geometry = distance

; Select components for the pull vector. default: Y Y Y

pull_dim = N N Y

; Cylinder radius for dynamic reaction force groups (nm)

pull_r1 = 1

; Switch from r1 to r0 in case of dynamic reaction force

pull_r0 = 1.5

pull_constr_tol = 1e-06

pull_start = yes

pull_nstxout = 10

pull_nstfout = 1

; Number of pull groups

pull_ngroups = 1

; Group name, weight (default all 1), vector, init, rate (nm/ps),

pull_group0 = Protein

pull_weights0 =

pull_pbcatom0 = 0

pull_group1 = LIN

pull_weights1 =

pull_pbcatom1 = 0

pull_vec1 = 0.0 0.0 0.0

pull_init1 = 0.34

pull_rate1 = 0.0

pull_k1 = 837

pull_kB1 = 837

I've also tried cylynder geometry, changing pull_dim = ... but my water
still goes out.

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