[gmx-users] Coordinate file for lipid bilayer
jmsstarlight at gmail.com
Tue Oct 2 22:12:18 CEST 2012
This is exactly what I've obtained
the same effect was also in case of intact tieleman's lipid bilayers (
the water layers were broader than lipid after resizing with genbox)
2012/10/2, Justin Lemkul <jalemkul at vt.edu>:
> On 10/2/12 3:49 PM, James Starlight wrote:
>> Previously I've expanded initial system on Z-dim before the protein
>> was inserted to increase both water layers.
>> After current processing with Genbox there is no problems in Z
>> actually- it look likes sandwich with two broader bread layers and
>> narrower cutlet :) So the lipid layer in x and y is thinker than water
>> ( so the lipid number stay the same after resizing).
> Posting a link to an actual image would be really useful here. I'm not sure
> understand your metaphor exactly.
> If you're looking to add lipids and water around an existing system, the
> z-dimension of the solute and solvent boxes have to be the same. So if you
> a system that you have extended in z to accommodate a protein or whatever
> you need to manipulate a DPPC-only system in the same way - extend its
> z-dimension to be the same as the "solute," maintaining the relative
> position of
> the membrane within the new "solvent" box, and then add water in the
> configuration to fill that box. Then proceed as I've suggested before. It
> should be obvious from all of this that it is vastly easier to plan a box of
> sufficient size before starting ;)
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users