[gmx-users] Steered Molecular Dynamics (SMD)

[toby10222224 at sina.com]

 Dear all:
These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I expected. Part of my .gro file and .mdp file are below. By& using them, the COM of the slab of griphene moved at a constant speed, but the 'slab' crashed. Because not all the carbon atoms moved at the same speed.
In order to produce the results that I want, which pull type (no, umbrella, constraint or constant_force) and which pull geometry (distance, direction, cylinder or position) shall I use? There is no reference group in my simulation. Do I need to modify the .gro file?

Part of the .gro file:
...
 4917sla      C11093   1.265   1.609   0.237
 4918sla      C11094   1.549   1.609   0.237
 4919sla      C11095   1.336   1.486   0.237
 4920sla      C11096   1.478   1.486   0.237
 4921sla      C11097   1.691   1.363   0.237
 4922sla      C11098   1.975   1.363   0.237
 4923sla      C11099   1.762   1.240   0.237
 4924sla      C11100   1.904   1.240   0.237
 4925sla      C11101   2.117   1.363   0.237
 4926sla      C11102   2.401   1.363   0.237
...
These are all the carbon atoms of the slab of griphene.

The Pulling Code:
; COM PULLING          
; Pull type: no, umbrella, constraint or constant_force
pull                     = constraint
; Pull geometry: distance, direction, cylinder or position
pull_geometry            = direction
; 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               = no
pull_nstxout             = 10
pull_nstfout             = 10
; Number of pull groups 
pull_ngroups             = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0              = 
pull_weights0            = 
pull_pbcatom0            = 0
pull_group1              = sla
pull_weights1            = 
pull_pbcatom1            = 0
pull_vec1                = 0.0 0.0 1.0
pull_init1               = 0.237
pull_rate1               = 5e-4
pull_k1                  = 
pull_kB1                 = 

Any suggestions are welcome! Thank you in advance!