[gmx-users] Nonsymetric molecule across pbc

Steven Neumann s.neumann08 at gmail.com
Tue Feb 18 20:49:30 CET 2014


 The picture is confidential so I will send it to you in the separate msg.
The distance between all tubes e.g. is 10 nm at the picture (I will attach
polypeptides to them later on). So I want to run window at this distance...
Then decrease it every 0.2 nm so all distances will decrease between
them...(3 tubes COM makes always isosceles traingle). I need to pull all of
them somehow closer to each other with some constraints or distance
restrarints I think...to reaach 9.8 nm etc.  So I wish that the reaction
coordinate would be the distance between all of their surfaces. Do you know
what I mean? Or maybe build something easier...they all matter and will
have influence on the distance... hence no clue which one of them apply
with harmonic potential...


On Tue, Feb 18, 2014 at 7:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
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