[gmx-users] CNT ROTATION

[Dr. Vitaly Chaban]

This sounds too crazy for me.

Do you have an image of your MD box?

What does 3nm mean for your box? Half of any side?

Dr. Vitaly V. Chaban


On Mon, May 26, 2014 at 8:56 PM, ANDRES ADOLFO ORTEGA GUERRERO
<andres.ortega at correounivalle.edu.co> wrote:
> 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
> channel,
> 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
> SWCNT ,
>
> 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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