[gmx-users] Query regarding energy minimization for packing the lipids around the protein

Anushree Tripathi anushritripathi at gmail.com
Wed Jan 25 11:32:59 CET 2012

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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