# [gmx-users] Quasi-Harmonic entropy and g_covar

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Thu Oct 28 18:50:11 CEST 2004

```---- Message from Nguyen Hoang Phuong
<phuong at theochem.uni-frankfurt.de> at 2004-10-28 18:38:13 ------
>
>
>> 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).
>

I agree with this. It is necessary to remove rotational and
translational motion by fitting to a structure. You could argue that
it is better to fit to the average of your equilibrated frames, as
this is in some way the centre of your quasi-harmonic motion, but I
don't think this makes a significant difference in most cases. Worth
trying though.

Dave Evans

>Phuong
>
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```