[gmx-users] Re: Membrane Simulation

Justin Lemkul jalemkul at vt.edu
Fri Apr 19 13:48:33 CEST 2013

On 4/19/13 7:37 AM, Giuseppe wrote:
> Dear Justin,
> thank you very much for replying. When I run the editconf tool I set for
> sure the right box vectors (6.23910   6.17970   6.91950) so that in the
> system.gro file (according to the nomenclature of your tutorial) the box
> vectors from the protein structure and from the membrane are the same, but i
> noticed that, after using the perl tool, they magically changed (e.g. in the
> system_inflated.gro file they became 24.95640  24.71880   6.91950). Maybe

That's not magic, it's what InflateGRO does.  It expands the membrane outward, 
thus changing the box vectors.

> something is wrong with the "-center" option? I include the complete
> editconf command that I run: "editconf -f protein_processed.gro -o
> protein_newbox.gro -c -box 6.23910   6.17970   6.91950 -rotate 85 -10 55
> -center 8 8 6". Thanks for your patience and your appreciated help.

Here's your problem.  First, -c and -center do not play well with one another. 
The -c option centers the protein at (vector/2) in each dimension.  Then you're 
manually specifying a center with -center, so -c is overridden.  Moreover, the 
values provided to -center make no sense, since they place the protein outside 
of the box.  Either use -c or a sensible setting for -center, whichever makes 
sense in your case.



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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