[AMBER] Reorienting the protein during simulation

From: Ahmed Mashaly <mashaly_1988.yahoo.com>
Date: Tue, 16 Jan 2018 10:52:20 +0000 (UTC)


I am using a very long protein in a rectangular box, the protein at the beginning is oriented along the main axes and based on it, the water box too is aligned to the same main axes. But with simulation, it rotates horizontally and gets out of the box from both sides while the water box is maintained at the main axes. I recenter it every 5 ns because of the water diffusion outside, but the orientation doesn't change to the original state and it starts getting out after 20 ns.
This is what I use for recenteringtrajin my_rst_file.rautoimagecenter: 1-1500 mass originimage origin center
I also tried to addprinicipal :1-1500 dorotation mass
but it rotates the whole system and not to the main axes, so I get the same result of the protein outside the box ... So, any suggestions?

Kind Regards,Ahmed

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Received on Tue Jan 16 2018 - 03:00:02 PST
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