[gmx-users] CNT ROTATION

ANDRES ADOLFO ORTEGA GUERRERO andres.ortega at correounivalle.edu.co
Mon May 26 20:58:39 CEST 2014

Hi dear Gromacs User,
I have done a pulling simulation of a SWCNT against an ion channel(the
SWCNT , and the ion channel pore's are the same), in order to study
the interaction between SWCNT and the outside (extracellular side) of the
So i put the SWCNT about 3nm of distance from the ion channel, so the SWCNT
starts going down straight (against ion channel) but there's a distance
where the SWCNT just doesn´t go down, and starts to rotate in its own
axis(Z in this case) , and tried to go down, just that it continue rotating
and starts to turning,

I was thinking that this behavior was due to the hydrophobic nature of the

i was wondering if you have any idea of this, or if this is ok, i tried a
force of 800 and the result was the same

pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
;pull_vec1       = 0.0 0.0 1.0 ;
pull_start      = yes
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     =CNT
pull_init1      = 0
pull_rate1      = -0.1
pull_k1         = 1000      ; kJ mol^-1 nm^-2

thank you in advance

Andres Ortega
Universidad del Valle (Colombia)

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