[gmx-users] Re: Lipid-protein simulation....
ramadavidgroup at gmail.com
Tue Jun 26 18:08:01 CEST 2012
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
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
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