[gmx-users] Box dimension in Umbrella Sampling

[Justin Lemkul]

On 4/25/19 7:10 AM, SUSHMITA BASU wrote:
> Dear users,
> I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. I understand why for a pull of 5nm, the z axis of the box is set at 12 nm, but did not get how the x and y axis of the box is determined. This question might be very basic, but I cannot figure out how to do it. Kindly help me in this. Thanks in advance.

I built a standard box with editconf -d and then used the x and y box 
vectors and extended along z.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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