[gmx-users] [EXT] Re: Water in hydrophobic core of POPC lipid bilayer

[Smith, Iris]

Hi Dallas,

Thank you so much for your expedient response. I increased the radius from 0.375 to 0.600 however upon solvation, the water filled the hydrophobic core again, albeit not as much as the initial solvation (at radius 0.375 added 6338 water molecules; at radius 0.600 added 4672 water molecules).

Should I increase the radius again until it pushes all the water out? If so, by what increment?

Iris

 

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | (216) 445-7885
 
 

On 6/4/18, 12:42 AM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Dallas Warren" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of dallas.warren at monash.edu> wrote:

    Iris, simply increase the radius until the water is excluded. This
    parameter has no impact on the simulation, just where the water molecules
    can be placed when it is being solvated
    
    
    On Sat, 2 Jun. 2018, 7:21 am Smith, Iris, <smithi4 at ccf.org> wrote:
    
    > Hello,
    >
    > I have successfully completed the KALP-15 in DPPC membrane tutorial
    > recently and have since moved on to setting up my own protein-membrane
    > system.
    >
    > For my system I am using POPC lipid parameters with GROMOS 53a6 ff
    > obtained from the Lipidbook (2010 Poger and Mark version). After solvating
    > my system, water flooded the hydrophobic core within the POPC lipid
    > bilayer.  I have modified the vdw for the carbon atoms by increasing from
    > 0.15 to 0.375. However, I don’t want to arbitrarily increase the vdw again
    > without possibly causing artificial voids around my protein.
    >
    > Can someone offer suggestions? Thank you for your help.
    >
    > Best,
    > Iris
    >
    >
    >
    >
    >
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Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.