[gmx-users] Quasi-Harmonic entropy and g_covar

[Nguyen Hoang Phuong]

> I tried to calculate the quasi-harmonic entropies from an MD simulation
> from the covariance matrix, using g_covar as follows:
> (1). Using the -nofit flag
> (2). After fitting the coordinates to the initial configuration
>
> When examining the eigenvalues, I got 3N eigenvalues for (1) and 3N-6
> for (2) - i.e. the last 6 values were several orders of magnitude
> smaller than the eigenvalues just prior to them, and some were negative
> (and still, very close to zero).
>
> According to Andricioaei and Karplus (J Chem Phys 115: 6289), one needs
> to use 3N-6 degrees of freedom in order to calculate the entropy in a
> quasi-harmonic representation. Hence, my questions are:
> 1. Should I expect to find the difference in the number (and magnitude)
> of eigenvalues in (1) and (2), or is there a problem with the accuracy
> of the simulation?
> 2. Which eigenvalues should I use?
> 3. If I use the eigenvalues obtained from (2), do I account for all
> degrees of freedom or just for the vibrational?
>
> I'd appreciate any comments,

You should expect to find the difference in the number (and magnitude)
of eigenvalues in (1) and (2).

you should use the eigenvalues obtained from (2) for the
vibrational entropy. There is the mixing between vibrational motions and
rotational motion in (1). This mixing is shown in the last 6 eigenvalues
obtained from (1).

Phuong