[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222224 at sina.com)

toby10222224 at sina.com toby10222224 at sina.com
Wed Jan 27 05:50:49 CET 2010


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:
...
 4876sla      C11052   3.608   0.748   0.237  0.0000 -0.0000  0.0001
 4877sla      C11053   3.821   0.871   0.237  0.0000 -0.0000  0.0001
 4878sla      C11054   0.000   0.871   0.237  0.0000 -0.0000  0.0001
 4879sla      C11055   3.892   0.748   0.237  0.0000 -0.0000  0.0001
 4880sla      C11056   0.017   0.748   0.237  0.0000 -0.0000  0.0001
 4881sla      C11057   3.395   1.117   0.237  0.0000 -0.0000  0.0001
 4882sla      C11058   3.679   1.117   0.237  0.0000 -0.0000  0.0001
 4883sla      C11059   3.466   0.994   0.237  0.0000 -0.0000  0.0001
 4884sla      C11060   3.608   0.994   0.237  0.0000 -0.0000  0.0001
 4885sla      C11061   3.821   1.117   0.237  0.0000 -0.0000  0.0001
 4886sla      C11062   0.000   1.117   0.237  0.0000 -0.0000  0.0001
...
These are all the carbon atoms of the slab of griphene.
 
; 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!
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