[gmx-users] Quasi-Harmonic entropy and g_covar

[Ran Friedman]

Dear GMX users,

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,
Ran.

-- 
------------------------------------------------------
Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
------------------------------------------------------