**From:** Mortimer Hemmit (*mortimer.hemmit_at_gmail.com*)

**Date:** Wed Sep 02 2020 - 20:02:03 CDT

**Next message:**Alex Balaeff: "Re: Re:Re: Wrong number of basis-sets stored!"**Previous message:**辛志宏: "Re:Re: Wrong number of basis-sets stored!"**In reply to:**Jérôme Hénin: "Re: Colvars Harmonic Bias Force Direction"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Jerome,

Thank you very much, it makes a lot more sense now. The visualization

with the dashboard was very helpful.

Mortimer

On Wed, Sep 2, 2020 at 9:03 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

*>
*

*> Hi Mortimer,
*

*>
*

*> If x are the Cartesian coordinates of atoms, let's define a collective variable f(x).
*

*> A harmonic potential on the colvar, centered on f0 and with force constant k will be:
*

*> V(x) = 1/2*k*(f(x)-f0)^2
*

*>
*

*> This is a function of x indirectly, through the function f(x). The corresponding force on atoms is the negative gradient of the potential with respect to atomic positions x:
*

*> F(x) = - dV(x) / dx = - k * (f(x)-f0) * df(x)/dx
*

*>
*

*> Here df(x)/dx means the gradient of the colvar with respect to Cartesian coordinates x. That's a vector pointing in the direction in Cartesian coordinates along which f(x) increases the fastest.
*

*> The magnitude and direction of the force also depend on the magnitude and sign of (f(x)-f0), that is where the colvar is with respect to the set restraint center.
*

*>
*

*> So to summarize, the biasing force will be applied in the direction that causes the maximum change in the value of the colvar.
*

*>
*

*> If you use the latest VMD under Linux, you can easily visualize the gradients of any scalar colvar using the Colvars Dashboard plugin.
*

*>
*

*> Best,
*

*> Jerome
*

*>
*

*>
*

*> ----- On 2 Sep 20, at 14:28, Mortimer Hemmit mortimer.hemmit_at_gmail.com wrote:
*

*>
*

*> > Hello,
*

*> >
*

*> > I am performing some steered molecular dynamics simulations. I was
*

*> > wondering how the harmonic biases worked.
*

*> >
*

*> > I understand how a simple colvar with a harmonic bias on the distance
*

*> > between atoms could work. I can picture it as a spring attached
*

*> > between the atoms which exerts a force that pulls each atom towards
*

*> > the other.
*

*> >
*

*> > However, for more complicated colvars such as radius of gyration,
*

*> > coordination number, dihedral angle, RMSD, to name a few, how exactly
*

*> > does the added potential manifest itself to restrain these quantities
*

*> > to their desired values? In which direction do the forces/springs
*

*> > point (or are there even forces at all) if I put a harmonic bias on
*

*> > these colvars?
*

*> >
*

*> > I have looked at the user guide and the Colvars paper, but I am still
*

*> > confused about the forces.
*

*> >
*

*> > If anyone could help me clear this up or point me in the right
*

*> > direction with some references, that would be greatly appreciated.
*

*> >
*

*> > Thank you very much,
*

*> > Mortimer
*

**Next message:**Alex Balaeff: "Re: Re:Re: Wrong number of basis-sets stored!"**Previous message:**辛志宏: "Re:Re: Wrong number of basis-sets stored!"**In reply to:**Jérôme Hénin: "Re: Colvars Harmonic Bias Force Direction"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Fri Dec 31 2021 - 23:17:09 CST
*