Hello,
It is not a really problem, since the water will move during the simulation
(due to the hydrophobic effect), but It may take for that all the water left
the micelle center. So I suggest you to use genbox with the following arguments
-shell or -vdwd (see the genbox manual).
An other approach if you use Packmol to construct your micelle is to reduce the
space between the SDS alkyl chains during the construction process by palying
with the value in the inside command in your packmol script
# atoms 39 is the last Carbon of the C12 alkyl chain for CHARMM
atoms 39
inside sphere 0. 0. 0. 3.0 <--- 3 is the distance (in A) between the
micelle center and the 12th carbon of the SDS alkyl chain. [1]
end atoms
[1] - 2-3 is a good value if you want to construct a SDS micelle with 60
monomers
- You will need the minimize carrefully the micelle to remove steric clashes
between SDS chains
HTH
------------------------------
Message: 3
Date: Mon, 29 Dec 2014 11:09:18 +0330
From: Mina Hashemi <hashemi.mi...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] how to remove water molecule inside micelle?
Message-ID:
<CAFYjG+ad2XDVy3PEO9Xnd6E9=n6qsv9srgtkk8sjr0honoh...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear gromacs users
I prepared my simulation system containing SDS.
Then I added water molecules using genbox. Some water molecules
entered in to the micelle.
How to remove water molecules inside the micelle?
Any help will highly appreciated.
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