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

Dallas Warren dallas.warren at monash.edu
Mon Jun 4 06:41:39 CEST 2018

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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