[gmx-users] Rotation Constraints - PMF

[Carsten Kutzner]

Hi Anna,

please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual.
You can restrain the angle of rotation about an axis by setting the rotation rate
to zero. There is also a 4.5 add-on available with rotational restraints in
the Gromacs git repository (branch "rotation"). For more info you may want to
look at this page:

http://www.mpibpc.mpg.de/grubmueller/rotation

Best,
  Carsten


On Jul 23, 2013, at 12:18 PM, battistia at libero.it wrote:

> Dear user and expert,
> I'd like ask you a suggestion about a problem that I will try present you schematically.
> I have got a structure "s" and I have generated the topolgy file itp for it.A number of separate "s" in turn generate a complex structure A, that is characterized by a cylindrical shape.
> Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 "s" structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B.
> 
> My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics.
> So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction.
> 
> It this possible?  If it is so, could you tell me how to do that?
> Than you very much,
> Anna
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa