[gmx-users] Error during CNP simulation

Bharath K. Srikanth s.bharath at iitg.ernet.in
Sun Oct 28 20:25:10 CET 2012

Hi everyone,

I'm trying to simulate the diffusion of a coarse-grained carbon
nanoparticle (from Monticelli) into a coarse-grained DOPC lipid bilayer,
to reproduce the results obtained by Wong-Ekkabut et al. I first assembled
my bilayer in a box of size 7.5 x 7.5 x 7.5 nm3, and the results appeared
legitimate. However, I'm now trying to repeat the experiment by placing
the carbon nanoparticle at an initial position further away from the
bilayer, and so I've resized my box to 15 nm x 7.5 nm x 7.5 nm.

In this case, what happens is that after solvation using genbox, if I
carry out an energy minimization, the CNP drifts very close to the
bilayer, rendering my increase of the box size redundant. To overcome
this, I've tried restraining the positions of the CNP and the bilayer, but
when I do this, my simulation 'blows up'. I'm not aware of how to overcome
this problem. Would you be able to help me with this?


Bharath K Srikanth

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