[gmx-users] simulation box size

Aditi Borkar aditi.borkar at gmail.com
Tue Sep 15 11:18:14 CEST 2009

Dear All,

While simulating a protein in a box of solvent, I know that the box
size should be twice the length of the cut-off. So, if I am using a
van der Waals cutoff of 1.4, does it mean that the box dimension
should be atleast 2.8 nm from the periphery of the protein?

Secondly, in the experimental conditions, my protein concentration is
1 mM. This accounts to 1 protein molecule occupying 1660 nm^3. For
such a volume, I have to generate a box with -d = 3.7 in editconf. I
feel that the box is too large and may compromise my computational
time. Please comment

-Aditi Borkar,

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