[gmx-users] Steered Molecular Dynamics (SMD)

2010-02-25 Thread toby10222224
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

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

2010-01-22 Thread Carsten Kutzner
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,

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

2010-01-21 Thread toby10222224
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