[gmx-users] Rotation Constraints - PMF

battistia at libero.it battistia at libero.it
Tue Jul 23 12:18:37 CEST 2013

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,


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