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

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================