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

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 8 23:39:50 CEST 2012

On 6/8/12 5:32 PM, Erica Hicks wrote:
> Hi,
> 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?

Make sure you added the correct topology information (step 2 in the tutorial, 
note the green text):


Step 3.2 tells you:

"Remove unnecessary lines (the box vectors from the KALP structure, the header 
information from the DPPC structure) and update the second line of the 
coordinate file (total number of atoms) accordingly."

The tutorial assumes you're familiar with such operations, so in reality what 
it's implying is that, since you've now concatenated a protein and a 128-lipid 
membrane, you need to add:

DPPC 128

to the [molecules] directive (after the Protein line to keep the correct order). 
  Further manual modifications are necessary based on how many lipids InflateGRO 


> Erica
> ________________________________
> 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
> --
> ========================================
> 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
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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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