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

[Smith, Iris]

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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