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

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

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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