[gmx-users] Re: Energy Minimization - not getting correct lipid area

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 8 23:00:14 CEST 2012

On 6/8/12 4:57 PM, Erica Hicks wrote:
> It was after just one iteration. The number of lipids removed after scaling
> the lipids by a factor of 4 was two. I am not sure how to update this as the
> [molecules] directive in the topology.top shows only the number of moles,
> i.e. 1.

The number shown in [molecules] is the number of molecules of a given species. 
If you started with 128 lipids, a removal of 4 means you need to list 124 lipids.

I don't know how you can get such a small area with only one iteration of 
shrinking.  Your box should be enormous at that point.



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


More information about the gromacs.org_gmx-users mailing list