[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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