[gmx-users] SWCNT interaction with the outside of an ion channel

[Andres Ortega]

Hi dear gromacs users, 

I am planning to study the interaction between a SWCNT and the outside of an
ion channel, 
in order to do this i am preparing a Umbrella Sampling Simulation, were i
put the CNT, (3nm or 2nm) from 
the ion channel's pore, and the CNT axis is parallel to the pore axis, in
order to compute the PMF between the CNT and the external residues of the
ion channel , 

in order to do this i was thinking first just run unconstrained MD of the
CNT and understand the potential energy surface, and then run the US using
constraints XY (Z axis) due to CNT might move or should i not use 
constraints at running US ? , 

I was wondering if you could give me some advice about this, it is my point
of view well think? or should i think in a different methodology ? 

Thank you in advance 

Andrés

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