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## Re: [ESPResSo-users] VIRTUAL_SITES

 From: Dudo Subject: Re: [ESPResSo-users] VIRTUAL_SITES Date: Mon, 8 Sep 2014 14:57:56 +0200

Hi,

please is it possible to set a virtual particle in the center-of-mass of each two consecutive real particles in a polymer chain?
Am I right that in such the case a given virtual site would need to be part of two molecules?
Do the sites stay in the COM, or are their positions being updated within the simulation?

(R)-(VCOM)-(R)-(VCOM)-(R)-...-(R)

Thanks
D.

On Thu, Aug 21, 2014 at 5:06 PM, Rudolf Weeber wrote:
Hi,
On Thu, Aug 21, 2014 at 04:50:33PM +0200, Dudo wrote:
> please, I would need a sort of under the hood information,
> do the virtual sites have mass and gamma or only if VIRTUAL_THERMOSTAT is
> called?
The mass property of virtual sites is ignored, as they are not propagated using Newton's eqn of motion.
Rather, their position is calculated from the position and orientation of the particle, they are related to, i.e., the particle in the center of mass of the rigid body.
Unless you set the switch mentioned above, virtual sites are not thermostated. Instead, the thermostating is done through the rotational and translational degree of freedom of the particle in the center of mass of the rigid body.
If you want correct dynamics, you will probably need to set
mass of the particle in the rigid body's center of mass =total mass of all particles forming the rigid body.
Interial tensor fo the particle in the center of mass = Inertial tensor of the rigid body as a whole.
Here, it is important to make sure that the orthogonal basis in which you specify the inertial tensor co-insides with the co-rotating frame of reference of the particle in the center of mass.
The easiest way to achieve this, is to set the quaternions of the central particle to 1 0 0 0.
In this case, the co-rotating frame of reference is equal to the lab frame.

If you only need static properties, you can ignore the mass andÂ  inertia of the particle in the center of mass.

It is currently not possible to set the gamma parameter of the Langevin thermostat independently for the rotational and translational degree of freedom.

Hope that helps.
Regards, Rudolf

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