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lqz Offline OP
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Dear all:

I have a protein embedded inside a lipid bilayer, which formed a water channel, and I can see some water molecules passed the lipid bilayer through the protein. Is there a way to count the number of water molecules really cross the bilayer? I can see a lot of water molecules did not cross the bilayer but only reached the center of the bilayer, then moved back. Thank you.

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Since there is no "count crossing waters"-command in CHARMM (yet), you could post a mathematical description (ie, science!) of what you want to do, and hope that somebody can then hint at CHARMM commands that may be useful in order to achieve your goal. The most difficult part here is the science, so you may want to consult your supervisor...


Lennart Nilsson
Karolinska Institutet
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I've just posted some files from a work flow I've used for counting waters that transit the bilayer in the Script Archive.


Rick Venable
computational chemist

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lqz Offline OP
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That is a great news, Rick. Thank you!


Moderated by  BRBrooks, lennart, rmv 

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