Dear all,
i have a couple of questions about using packmol.
(1) how to follow these descriptions: ˇ°If you have large molecules, try running the program twice, one to pack these molecules, and then use the solution as fixed molecule for the next packing, in which solvation is included. This may be particularly useful for building solvated membranes. Build the membrane first and then use it as a fixed molecule for a solvation run.ˇ±
is the example below able to demonstrate above words?
------------------------------------------------------------
tolerance 2.0
filetype xyz
output interface.xyz
structure water.xyz
number 1019
inside box -20. 0. 0. 0. 39. 39.
end structure
structure chlor.xyz
number 199
inside box 0. 0. 0. 21. 39. 39.
end structure
structure t3.xyz
centerofmass
fixed 0. 20. 20. 1.57 1.57 1.57
end structure
(2) as for the above example, when I execute the packmol on it, I find that there is a rather significant vacuum region around the fixed molecule. Is it normal or abnormal? how to remove the vacuum and reach an real enclosure?
thank you very much!
Junjian Miao
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Received on Thu Apr 07 2011 - 07:30:04 PDT
