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

[rama david]

On Tue, Jun 26, 2012 at 9:32 PM, rama david <ramadavidgroup at gmail.com> wrote:
> 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
 I deleted SOL molecule from DPPC layer, I plan to solvate  system
after catenation
of lipid and protein gro file).
> 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
> Rama