[gmx-users] problem with making index.ndx

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 31 12:59:42 CET 2012

Anushree Tripathi wrote:
> I am using gromacs 4.5.3 version.When I run the command (i.e., make_ndx 
> -f em.gro -o index.ndx),It is not showing any option for DPPC group 
> which I want to include.Please tell me how could I merge or create this 
> option for proceeding to the next step of NVT simulation.

Every individual molecule that is not in a default group like Protein in the 
system is given its own group.  The fact that DPPC does not show up in your list 
suggests to me that you have no DPPC in your coordinate file.  Sounds to me like 
you're using an .mdp file designed for membrane protein MD when you don't have a 
membrane present.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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