[gmx-users] g_membed mdp file

[Yogesh Sharma]

Sir,

I tried using  inflategro but bash script is not compatible with my version
i guess.
I am getting error

########################################## RUNNING SHRINKING ITERATION
{1..26}...#########################################run_inflategro.sh: 32:
run_inflategro.sh: Illegal number: {1..26}*

With manual procedure, I am little confused ... Do I have to repeat
from step 2 to step 4 for next  26
iterations?

1.perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
2.gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p
topol.top -r system_inflated.gro -o system_inflated_em.tpr
  gmx mdrun -deffnm system_inflated_em
3.gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o
tmp.gro -pbc mol
  mv tmp.gro system_inflated_em.gro
4.perl inflategro.pl system_inflated_em.gro 0.95 DPPC 0
system_shrink1.gro 5 area_shrink1.dat

for example

2.gmx grompp -f minim_inflategro.mdp -c *system_shrink1.gro* -p
topol.top -r *system_shrink1.gro* -o *system_inflated_em1.tpr*
  gmx mdrun -deffnm *system_inflated_em1*
3.gmx trjconv -s *system_inflated_em1.tpr* -f
s*ystem_inflated_em1.gro* -o *tmp1.gro* -pbc mol
  mv *tmp1.gro system_inflated_em1.gro*
4.perl inflategro.pl *system_inflated_em1.gro* *0* DPPC 0
*system_shrink2.gro* 5 *area_shrink2.dat*


*......... and so on.. until I reach area per lipid around 70 angstrom
square? *