[gmx-users] Nonsymetric molecule across pbc

Justin Lemkul jalemkul at vt.edu
Tue Feb 18 20:17:46 CET 2014

On 2/18/14, 1:37 PM, Steven Neumann wrote:
> Thanks a lot!
> Can you please give me a hint how to apply umbrella sampling to the system of 4
> nanotubes with pbc across xyz so that they infinite in length in z coordinate
> and 2 of them placed with its half to the unit cell copied across y
> coordinate...  I want to see PMF minima (equilibrium distance) between their
> centre of mass... With 2 nanotubes that would be easy (your tutorial) but with 4
> of them? I am thinking of changing the distance between and run windows but no
> clue which group setup as group0 and group1...

It's not clear what your objective really is, and I'm sorry to say that I find 
your description to be very confusing.  A picture would help.  What is your 
reaction coordinate?  Are you trying to determine the free energy profile for 
one tube in relation to another, with 2 others as bystanders, or do the other 2 
serve some functional role?  If you're looking to do a multidimensional WHAM, 
you'll have to approach each reaction coordinate individually.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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