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

Erica Hicks erica.hicks at my.und.edu
Fri Jun 8 23:32:10 CEST 2012


I went back and found that a possible error could be that the coordinate file was not updated correctly. After concatenated the Kalp_newbox.gro and dppc128_whole.gro, it said to update the coordinate file with the correct number of atoms. This should be the topology.top, right? But when I look through this, all I find is:
[ molecules ]
; Compound        #mols
Protein             1
Where should the number of atoms be and is topology.top the correct file?

From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998239h28 at n6.nabble.com]
Sent: Friday, June 08, 2012 4:02 PM
To: Hicks, Erica
Subject: Re: Energy Minimization - not getting correct lipid area

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

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