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

Fri Jan 22 07:41:47 CET 2010

&nbsp;
Dear all:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right?
3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; How to give the “pull_weights1” to avoid the above ERROR? 
Any suggestions and answers are welcome. Thank you in advance!
&nbsp;
; COM PULLING&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; 
; Pull type: no, umbrella, constraint or constant_force
pull&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= constant_force
; Pull geometry: distance, direction, cylinder or position
pull_geometry&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= distance
; Select components for the pull vector. default: Y Y Y
pull_dim&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;= N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 
pull_constr_tol&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; = 1e-06
pull_start&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= no
pull_nstxout&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; = 10
pull_nstfout&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; = 10
; Number of pull groups 
pull_ngroups&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; = 700
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;= 
pull_weights0&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 
pull_pbcatom0&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 
pull_group1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;= sla
pull_weights1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 1
pull_pbcatom1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 0
pull_vec1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; = 0.0 0.0 1.0
pull_init1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 0.0
pull_rate1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 0
pull_k1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;= 1.2e-4
pull_kB1&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;= 0
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100122/ae4655e0/attachment.html>