[gmx-users] g_membed mdp file

[Hamid Zaree]

I Don't grasp you.
You need change the for loop number to get the proper ApL (area per lipid)
and do not impelled to run every line in " run_inflategro .sh".
If you are a Linux user, this code easily implemented in terminal. For
windows users, a Perl or Python code is needed.
Maybe you didn't make this shell script executable in Linux.
You can do that by the following command (sudo chmod +x filename.sh) and
then run it through (./run_inflategro.sh).
-----------------------------------



On Tue, Dec 31, 2019 at 3:09 PM Yogesh Sharma <yogesh.rma13 at gmail.com>
wrote:

> 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? *
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