You show different atoms before and after minimization so this is not proof of
movement.
I often resize my box by changing the value at the end of the file and have
never had any problem with it. Of
course, you do need to be careful with this and everything you do.
Chris.
-- original message
Sorry Bharath, I simply can not believe that a macromolecule drifted 3 nm
during energy minimization.
What happened to the intervening solvent? I think that you have some problem
with your technique here.
Why did you use 120 constraints? Is this for bonds within the CNP?
You need to do 2 things
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 M
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
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