Dear all:
I’m using Gromacs-4.0.5 and I want to use
the pull code to pull a slab of griphene to move along the Z direction in the
simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms
and the positions of the 700 atoms are expected to be immobile in the X and Y
direction.
The following is the PULL CODE in my mdp file. However, when I used this code
for my simulation the error always came out as “Number of weights (1) for pull
group 1 'sla' does not match the number of atoms (700)”.
So here are my doubts about this simulation:
1. Can Gromacs-4.0.5 do this for me,
especially keeping the C atoms immobile in X and Y direction while moving along
the Z direction?
2. In my simulation, every carbon atom in
the slab of griphene was defined as a group. Is it right?
3. How to give the “pull_weights1” to avoid
the above ERROR?
Any suggestions and answers are welcome. Thank you in advance!
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull
= constant_force
; 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
=
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0
=
pull_constr_tol = 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 10
; Number of pull groups
pull_ngroups = 700
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0 =
pull_weights0 =
pull_pbcatom0 =
pull_group1 = sla
pull_weights1 = 1
pull_pbcatom1 = 0
pull_vec1 =
0.0 0.0 1.0
pull_init1 = 0.0
pull_rate1 = 0
pull_k1
= 1.2e-4
pull_kB1
= 0
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