[gmx-users] Quasi-Harmonic entropy and g_covar

[david.evans at ulsop.ac.uk]

>> 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.
>
>usually about the first 10 eigenvalues (low frequencies) contribute
>significantly to the entropy since entropy is proportional to
exp(-hbar*omega/KT). If the
>frequency omega is large, i.e small eigenvalue then the value
>exp(-hbar*omega/KT) is essentially zero.
>
>The mixing between vibrational motions and overall rotation is large
>for low frequency modes.
>
>>From above arguments, I think that the entropy will be different in
two
>cases, but one should try as you said.
>
Yes, I agree that it will definitely make a difference whether you
fit or not. I was suggesting that he try fitting to different
structures, and see if that affects the results. Maybe that wasn't
clear :)




>Phuong
>
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