[gmx-users] Quasi-Harmonic entropy and g_covar

Ran Friedman ran at hemi.tau.ac.il
Fri Oct 29 01:02:53 CEST 2004

Thanks a lot for your answer.

1. I run the simulations with the center of mass motion removal. Do I 
miss the translational motions altogether?
2. If the answer to my first question is true, does the different 
between the two calculations described below, i.e. with and without fit, 
correspond to the rotational contribution to the entropy?
3. Can I calculate the overall entropy from the simulation?


Nguyen Hoang Phuong wrote:

>>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).
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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

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