[gmx-users] Cutoff value during lipid shrinking using inflategro.pl script

[Justin A. Lemkul]

Jignesh Patel wrote:
> Hello all,
> 
> I am trying to do shrinking of lipids using inflategro.pl 
> <http://inflategro.pl> script. So anyone can suggest me *how much cut 
> off value* should I give to remove overlapped lipid residues. I have to 
> give *cutoff from starting step or at final step* of shrinking. 

You shouldn't be removing lipids when scaling your system down.  If you do, 
you'll keep deleting lipids until you have none left.

Have you gone through my membrane protein tutorial?  In it, I describe exactly 
how I usually go about running InflateGRO.

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

-Justin

> 
> perl    inflategro.pl <http://inflategro.pl>    confout.gro    0.95   
>  DPPC *   0   * system_shrink1.gro     5      area_shrink1.dat
> 
> Thanking You in anticipation.
> 
> -- 
> Best Wishes,
> Jignesh Patel
> M.S.(Pharm.),
> Center for Pharmacoinformatics,
> NIPER,
> S.A.S. Nagar,
> India
> 

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

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

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