[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Ok, James thank you
> 
> It seems that I should to wite some script for too many iterations e.g
> 
> perl inflategro.pl <http://inflategro.pl> minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat
> 
> grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr
> 
> mdrun -v -deffnm minimized2
> 
> perl inflategro.pl <http://inflategro.pl> minimized2.gro 0.95 DPPC 0 shrinked2.gro 5 area_shrink1.dat
> 
> grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr
> 
> mdrun -v -deffnm minimized2
> 
> ......
> 
> perl inflategro.pl <http://inflategro.pl> minimized20.gro 0.95 DPPC 0 shrinked20.gro 5 area_shrink1.dat
> 
> grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr
> 
> mdrun -v -deffnm minimized21
> 

All of which can be done in a for-loop instead of typing it out manually.

> Does this action sequence correct? So as the consequence I need to find operator wich stop the script untill defined value of S per lipid will be reached
> 

Yes.  You can read that value from the screen or from the area.dat file that 
inflategro.pl prints.

-Justin

-- 
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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

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