[gmx-users] Error during CNP simulation

Christopher Neale chris.neale at mail.utoronto.ca
Sun Oct 28 20:50:11 CET 2012

I presume that your 7.5 nm -> 15 nm resizing refers to the Cartesian dimension that lies along the bilayer normal?

Also, are you sure that the nanoparticle drifts significantly closer to the bilayer "during minimization", as you stated? That sounds unlikely. Perhaps this drift occurred during MD simulation after energy minimization?

How did you implement your restraints? My first try would be using the pull code harmonic restraints to restrain the distance between the center of mass of the bilayer and the center of mass of the nanoparticle, only applying the force along the dimension of your global bilayer normal. Note that, when doing this, the distance must always remain less than 1/2 of the box length along that dimension or your simulation will be unstable.

How did the system "blow up"? Was it a LINCS-based crash or massive expansion of the box or just that the bilayer fell apart? Did it blow up during energy minimization or MD simulation?


-- original message --

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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