Hi Carsten: Thank you for your answers. I don't know whether I am right to reply to gmx-us...@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! Hi,
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. Best, Carsten On Jan 22, 2010, at 7:41 AM, toby10222...@sina.com wrote: > Dear all: > Im 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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