[gmx-users] Re: Membrane Simulation
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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