[gmx-users] How to Run Energy Minimisation

[Justin A. Lemkul]

Nancy wrote:
> Hello,
> 
> More specifically, I am unsure as to the procedure of inflating and 
> minimizing a bilayer using "InflateGRO".  In the tutorial at:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
> 
> I followed it successfully up to the inflation step, but I do not know 
> specifically what parameters to run the energy minimisation.  Please advise.
> 

Most general EM .mdp files are suitable; a simple one is linked in Step 1 on the 
page you quote above, "Orient the protein and membrane;" modifications that 
should be made to it are described in Step 2, "Pack the lipids around the protein."

The caveat to my membrane protein tutorial was that the user should already be 
used to normal input/output routines with Gromacs.  A simpler tutorial to 
familiarize you with Gromacs procedures can be found at:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

It might be useful if you are unfamiliar with simulation protocols with Gromacs, 
since it is conceptually easier and more detailed in the description of each 
step. If the minimized bilayer is not showing up as inflated, then you probably 
invoked InflateGRO incorrectly (hence why I asked for the command lines you 
invoked).  Usage is described in the text of the inflategro.pl script, and I 
describe typical scaling factors that should be used for the procedure in the 
tutorial.

-Justin

> Thank you.
> 
> Nancy
> 
> 
> 
> 
> On Wed, Jul 29, 2009 at 7:49 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Nancy wrote:
> 
>         Hello,
> 
>         I am trying to run energy minimisation on a lipid bilayer
>         (downloaded from:
>         http://moose.bio.ucalgary.ca/files/dppc128.pdb).  I inflated the
>         bilayer using "InflateGRO" however, when I try to run the
>         minimisation, it seems to display the un-inflated bilayer.
>          Please advise.
> 
> 
>     Without seeing the command lines that you're issuing, we can only
>     assume you are doing something wrong.
> 
>     -Justin
> 
>         Thank you.
> 
>         Nancy
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

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

========================================