[gmx-users] pulling experiment

Xiaohua Zhang zhangxhcm at gmail.com
Mon Sep 20 03:57:32 CEST 2010

Dear gmx-users

I want to design such kind of computer experiment:

For a system composed of non-bonded three layers (carbon nanotubes,
graphene, or whatever), I want to fix layer0 (the group name) to exactly
(0,0,0), and pull layer2 by a constant force, for example, along positive x
all the time. The layer1 is free to move. I am confused to define the COM
pulling parameters, under the latest GROMACS 4.5.1, because it seems
possible to pull layer2
pull = constant_force
pull_geometry  =  direction_periodic
pull_ngroups  =  2
pull_group2 = layer2
pull_vec2 =  1.0 0.0 0.0
pull_k2 =  a number in unit kJ mol-1 nm-1
but how about group1 ?

Could you give me some suggestion?


Xiaohua Zhang

Suzhou Institute of Nano-Tech and Nano-Bionics
Ruoshui Road 398, Suzhou 215123, China

Phone: +86 512 62872552
Mobile: +86 137 71904040
Email: zhangxh at fudan.edu.cn
Email: xhzhang2009 at sinano.ac.cn
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