[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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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