[gmx-users] Implementing Radial Distance Constraints

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 17 20:29:54 CEST 2006

Bob Johnson wrote:
> Hello everyone,
> My system consists of a carbon nanotube and various chemicals that adsorb to the
> tube. I would like to use radial distance constraints to enforce adsorbates to
> maintain a fixed distance away from the nanotube. These restraints must obey
> the relation R = sqrt (x^2 + y^2) = user defined constant. With this type of
> restraint the adsorbates are free to move along the z and circumferential
> directions (something that can not be done with normal position or distance
> restraints).
> I would like to add a restraint potential given by V = 1/2*k*(R-R0)^2 = 1/2*k*(
> sqrt(x^2+y^2) - R0)^2. Here R0 is the fixed radial distance. Is this difficult
> to implement in Gromacs? What file in the source code would I edit?
> Thanks,
> Bob Johnson
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please be more clear.

if we assume your cnt is centered along the z-axis, given roughly by 
x^2+y^2 = d0. Am I correct in assuming that you want all other particles 
to have x^2+y^2 <= d1, where d1 < d0 ?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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