[gmx-users] Decreasing of the box size during membrane protein simulation

Justin Lemkul jalemkul at vt.edu
Mon Jan 28 14:39:51 CET 2013

On 1/28/13 8:30 AM, James Starlight wrote:
> Justin,
> Below you can see graph representation of my system after energy
> minimisation ( that case system was filled up with tip3p water using
> genbox  with slightly increased vdw for C atom ( to 2nm) to prevent

I'm assuming you mean 2 Angstrom?

> water movement into the membrane.
> http://img42.imageshack.us/img42/7213/b2armembrane.png

I can't exactly guess what the dimensions of the system are, but it seems to me 
that the z-dimension is not 10 nm based on a rough guess of how many lipids are 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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