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. For a pull of 5nm, the z axis of the box is set at 12 nm, that is fine 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.
Hi,
If I understood you correctly, you want to find out how big your box should be, right ? If yes, then answer is simple, you molecule shouldn't see it's period image upto a certain distance. At least the distance should be 3-3.5 (minimum) between periodic images of the molecule of the system.
Vikas Dubey Thanks for your response. As per the tutorial (Lemkuls' tutorial using gromacs) i have to manually define the box dimension. Now suppose i want to pull my molecule for 5nm along z axis, then the box dimension (XYZ) should be such that its z axis(or rather length) is > 10nm (double the pull distance), but what about the x and y axis (height and breadth) of the box? Again, may be am missing out on something very basic but kindly help me to resolve it.
Hey, Sushmita
From Gromacs umbrella sampling tutorial:
gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12
This is a command line from tutorial. -box 6.560 4.362 12 means x y z size.
Is this answer your question?
Please let me know if you have further question.
Hi Sushmita B,
The x and y dimensions should just be wide enough so that the protein or RNA doesn't see the periodic image of itself. Or in other words, you want the minimum distance between your protein in the box and protein in the periodic image to be greater than 2 nm, at the bare minimum, but 3 nm, to be safer. You can do this by first giving a command like this:
gmx editconf -f complex.gro -o complex_correct_XY.gro -c -d 1.5 -bt cubic
The latter command gets the correct x and y dimensions, centers the complex in the box, and puts 1.5 nm of space around the complex on all sides. If we open up the "complex_correct_XY.gro" file in a text editor like vi, then at the bottom, we'll find the dimensions of our box in x, y, and z. We'll want to remember the x and y dimensions for the next step. Let's say the file says the X & Y dimensions are 6 x 6 (nm).
Then, we'll want to set the correct Z-dimension for pulling. The Z-distance should be greater than double your pull distance. You're pulling 5 nm along the Z-axis. So you want the Z-dimension of your box to be greater than 10 nm. Let's say 12 nm. So, we'll use a command like this:
gmx editconf -f complex_correct_XY.gro -o complex_pull_ready.gro -box 6 6 12
The latter command will center our complex in a box with the same x and y dimensions that we previously showed were wide enough to prevent the complex from seeing it's periodic image. Then we also made it long enough in the Z-dimension for pulling.
Does that answer your question?
JD Tamucci Thanks a ton. This is exactly what I was looking for. I shall try this and update here if it works.
Jiajie Xu Thank you for your response. I had already mentioned that I was following that tutorial, but what I couldn't understand is that how those values were determined. JD Tamucci explained it nicely.
JD Tamucci It worked. In fact, instead of '-bt cubic' , i chose the default by not mentioning box type. It gave more accurate result.
Thanks once again.
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