[gmx-users] any alternative methods?

Justin Lemkul jalemkul at vt.edu
Wed Aug 22 15:16:54 CEST 2012

On 8/22/12 9:12 AM, Albert wrote:
> hello Justin:
>   thanks for reply.
>   I've read both the paper and manual script. As indicated from the output, I
> found the following line:
> 368    4.295    3.8840018217
> I just wondering how could it possible fro residue 368 with a value of 3.88?

My guess would be that this particular lipid is probably bound very tightly to 
some protein residue, which leads to the protein and lipid both contributing to 
the lateral area in that region.  In this case, the protein contributes more 
area than the lipid does.  You should look at the coordinate file and see what 
this residue is doing.

> For the pure lipids/water case, my apology for this since I forgot to change the
> box size values but the protein/lipids case is with correct box size.

That's good news.  It's always alarming to hear someone say that your work may 
not be reliable when you've done lots of work to ensure that it is ;)



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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