[gmx-users] how to remove water molecule inside micelle
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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to remove water molecule inside micelle?
it's hard to say without knowing how you prepared and relaxed your micelle before adding water, so I can only provide you a few general comments: (1) a properly relaxed, well-packed micelle should not present any voids and water should not go inside the micelle (check the literature, this has already been done a number of times already for SDS and other surfactants) (2) increasing the value for -vdwd should decrease the number of water molecules inside the micelle, even if the preparation step was not accomplished so carefully. (3) maybe you could try Packmol: http://www.ime.unicamp.br/~martinez/packmol/ On Mon, Dec 29, 2014 at 5:39 AM, Mina Hashemi hashemi.mi...@gmail.com wrote: 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to remove water molecule inside micelle?
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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
