[gmx-users] COM Pulling

Алексей Раевский rayevsky85 at gmail.com
Thu Jan 21 10:51:42 CET 2010


Hi all !

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
4.0.5...

protein - my substrate
LIN - my water

; COM PULLING

; 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),
kJ/(mol*nm^2)

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.

Thank you for help!
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