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

[Justin Lemkul]

On 6/6/18 11:38 AM, Smith, Iris wrote:
> 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).

Contact me off-list and I will send you a script that will remove the 
waters. It is clear that simply increasing radii is no longer an 
effective approach, likely due to changes in other atomic radii that 
have been implemented recently.

I will be updating my membrane protein tutorial with a better method.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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