[gmx-users] Lipid-protein simulation....

rama david ramadavidgroup at gmail.com
Tue Jun 26 18:02:16 CEST 2012

Hi Gromacs Friends,

 I completed Justin-Lipid Tutorial.
I plan to simulate protein-lipid system  to study protein-lipid interaction.
My Query is like

1. I plan to use DPPC (128) lipid from Tieleman Website.
  I removed its periodicity as per tutorial instruction..
  I found that I need the z box Dimension more than 6.59650.
  ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer).
So with help of editconf command I changed the Z box Dimension to 8.00
while  x and y are same .

Is these process is right or any good suggestion in my work-flow ???

2. I wish to put lipid membrane away from protein ( Protein is not
embedded in lipid ).
    Should I use InflateGro?? Should I use Strong position restrain
during Energy minimisation???

please give me valuable Guidance

With Best Wishes and regards

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