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

toby10222224 at sina.com toby10222224 at sina.com
Sat Jan 23 04:21:06 CET 2010

Hi Carsten:
Thank you for your answers. I don't know whether I am right to reply to gmx-users at gromacs.org. If I am wrong, please tell me.
As in my last letter, I said I was not able to set "pull_weights1" correctly. I have red the mannual, but I don't understand what it tells. I'll do with your recommendation, setting one pull group which contains 700 atoms and using Gromacs-4.0.7. Then how to set the "pull_weights1" ?
Best regards!

you should set one pull group, not 700. The number of atoms in your
pull group is 700. Freezing the pull group in x and y direction probably
does what you want. Please also consider to upgrade to 4.0.7,
which is the most recent stable version.


On Jan 22, 2010, at 7:41 AM, toby10222224 at sina.com wrote:

> 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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