[gmx-users] make-hole

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 18 17:05:17 CET 2009

Urszula Uciechowska wrote:
> Dear users,
> I am new to gromacs. I want to make a hole in center of lipid bilayer. My first question is... How can I 
> get the cx,cy and r values? Its not clear in the manual, and also lipat P8 how to know if its not lipat P6 
> etc. and what is lipid DMPC ? 

Your question is not well-formed.  How are you trying to make the hole?  Are you 
using the contributed mdrun_make_hole software?  If so, be aware that it is 
designed for an antiquated version of Gromacs (3.1.4).  If your goal is to 
incorporate a membrane protein, there are a number of more modern ways to go 
about it (see the wiki and posts within the list archives).

If you do not know what DMPC is, and you are trying to use it, you should stop 
and read some literature before blindly attempting a project.  There are also 
numerous simulation papers that label phospholipids within the introduction or 
methods sections, if you are curious about atom nomenclature.


> Thanks in advance for any help
> Best Regards,
> Urszula Uciechowska
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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