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

[Justin A. Lemkul]

On 6/26/12 12:02 PM, rama david 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).
> 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 ???
>

Changing the box dimensions to accommodate new species is fine.  By default, if 
you haven't used the -center option of editconf, the coordinates are position 
such that the solute is centered within the box.  This may or may not be what 
you want.  Check out the workflow and tips suggested here:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html

> 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???
>

The purpose of InflateGRO is to pack lipids around a protein.  If you don't need 
to embed the protein in the membrane, there is no point to using InflateGRO, or 
programs like g_membed.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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