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