[AMBER] radial distribution function mask

From: iccy liu <hbliu92.hotmail.com>
Date: Wed, 4 Mar 2009 18:57:08 +0000

Hi, all,

I am using ptraj to analyze my MD simulation results. I have a question about radial distribution. I would like to calculate the radial distribution function from the center of mass of my solute molecules. Can I do that using ptraj? I did try two things. first I select one atom in my solute molecule which I think is close to cms, and the plot is reasonable. I also tried to put the molecule name only as my mask (hoping ptraj would use center of mass in calculations), however the results are very strange. I wonder any experts can help me?

Thanks a lot,

Iccy Liu

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Received on Fri Mar 06 2009 - 01:12:55 PST
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