[gmx-users] using pull_geometry=cylinder for asymmetric pull-molecule

Justin Lemkul jalemkul at vt.edu
Mon Jan 26 13:55:44 CET 2015

On 1/26/15 4:37 AM, Alexandra Antipina wrote:
> Hello,users!
> I have a little question. I want to do PMF for system, where double helix DNA
> (its length approximately is 4 nm) is pulled to the lipid bilayer (its area
> approximately is 6nmX6nm). Molecule DNA is placed in parallel to the bilayer. It
> is known that in case lipid bilayer for the better to use
> pull-geometry=cylinder. My question is: This is correct use
> pull-geometry=cylinder,where pull molecule is long and asymmetric?
> Do I understand correctly that the only role of pull-geometry=cylinder to set
> accurate the reference group mass center?

If you're just studying the binding of DNA to a bilayer, you don't need cylinder 
geometry.  The cylinder geometry is only really useful when there is a specific 
microenvironment of interest from which the restraints are based.  Note the 
example in the manual is the extraction of a lipid from the bilayer, another 
might be passage of a molecule/ion through a membrane protein.  Binding of DNA 
to a membrane wouldn't require anything like this unless there is a specific 
microdomain/lipid cluster that is of interest.  If the membrane is homogeneous, 
you definitely don't need this.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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