[gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5

toby10222224 at sina.com toby10222224 at sina.com
Fri Jan 22 07:41:47 CET 2010

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100122/ae4655e0/attachment.html>

More information about the gromacs.org_gmx-users mailing list