Re: Problems with minimization

From: Diego Alejandro Vargas (
Date: Sun Nov 16 2008 - 00:28:53 CST


I never determined the dimensions and center of the protein alone. Following
the tutorial I used the Tk console in VMD to create the variable everyone
and used the commands "measure minmax" and "measure center" after I solvated
the protein. But the coordinates should be the same, right? (since water was
added to 20A in all directions based on coordinates of protein)

The values I obtained (rounded) were:
min max:
x: 13.63, 110.5
y: 29.65, 148.13
z: -37.25, 57.72

center (x,y,z): 61.963, 88.96, 10.165

As you can tell I rounded to the closest higher integer when defining
cellBasisVectors and to the closest integer when determining cellOrigin.
Which makes me realize I don't fully understand how cellBasisVectors are to
be determined: I defined the vector in each dimension to be half the length
of the system in that dimension.

Thank you for your response,

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