I have used "mdrun -v deffnm em" command for energy minimization just after running the command i.e., given below:
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat But When I run the command which is given below: Eeeeek! No confout.gro at all! Died at inflategro.pl line 81. Please guide me to troubleshoot the error. Also clarify the lines given in tutorial "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"):".
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