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I have a molecular dynamics trajectory of a micelle in a water box. For each frame, I want to get center of mass (COM) of the micelle and calculate the density of water molecules from COM to the sides of the water box. Does anybody know what is the best way to do that? I was wondering whether somebody has dealt with such an issue before.

Thanks Sadegh

XuMuK
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s110faramarzi
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  • Hi, Sadegh! Could you please explain in pictures what do you mean "and calculate the density of water molecules from COM to the sides of the water box"? And what lipids do you use? (Needed to write correct resname in example) – XuMuK Apr 05 '16 at 10:51

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First - a lot of useful commands and how to use them are written here.

You should select your lipids (I suppose micelle is build from phospholipids) than selecting by type - lipids:

set sel1 [atomselect top "lipids"]

or by resname : 

set sel1 [atomselect top resname DPC]

And than:

center_of_mass $sel1

calculate the density of water molecules from COM to the sides of the water box

I don't know what exactly you are talking about - there are some water molecules inside the micelle? Or waterbox is water molecules within certain distance from the micelle? Please, give some more info (better some pics of the system with descriptions).

XuMuK
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  • Hi XuMuK! the micelle is in a cubic water box, surrounded by water molecules. Also, some water molecules penetrate into the micelle interior. To see how many water molecules are inside and how many are outside of micelle, I need to calculate radial density function of water molecules with respect to micelle COM. You can imagine some spherical layers around micelle COM, with variable radii, r. I want to find the number of water molecules inside each of those layers as a function of r. However, I found out that LOOS package has a plugin that does that. – s110faramarzi Apr 05 '16 at 17:56
  • @s110faramarzi So you should use `atomselect top "within 5 of resname DPPC"` http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node108.html Also: http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_faq.html The way to do that is to specify something like 'sqr(x-3)+sqr(y-4)+sqr(z+5) < sqr(2)' which will select all the atoms within 2Å of the point (x,y,z)=(3,4,-5). We may someday add the selection 'within distance of point x y z to simplify this very common selection. – XuMuK Apr 06 '16 at 01:24