[gmx-users] how to remove water molecule inside micelle

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Mon Dec 29 12:25:19 CET 2014


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  



Message: 3
Date: Mon, 29 Dec 2014 11:09:18 +0330
From: Mina Hashemi <hashemi.mina5 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] how to remove water molecule inside micelle?
        <CAFYjG+ad2XDVy3PEO9Xnd6E9=N6qSV9sRgtkK8SjR0hoNOHUDQ at mail.gmail.com>
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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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