Re: [AMBER] huge values for the vibrational entropy from ptraj

From: David A Case <>
Date: Thu, 31 Oct 2013 07:44:22 -0400

On Thu, Oct 31, 2013, Vlad Cojocaru wrote:
> Below is a output snapshot ... I am guessing I am still far from
> convergence .

It is indeed very hard to converge quasiharmonic calculations. I'd again
suggest working with a smaller problem and making sure you understand how
everything works. Look at all the frequencies. The fact that you still have
NaN in the heat capacity field suggests some problems, and you total entropies
are not reasonable.

> warning: setting vibrational entropy to zero for mode 19056 with vtemp
> = -8049467.209940

This seems like more than a warning--something is quite wrong. Look at the
frequency and other data for mode 19056 -- do you really have this many
degrees of freedom? If so, you are trying to get results for a gigantic
system that is larger than any I have ever had success with. Are there
published calculations that do a similar analysis?

> freq. E Cv S
> cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
> --------------------------------------------------------------------------------
> Total 57372.075 -nan 23444.731
> translational 0.888 2.979 58.245
> rotational 0.888 2.979 62.369
> vibrational 57370.299 -nan 23324.117

Ditto for the numbers above.


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Received on Thu Oct 31 2013 - 05:00:05 PDT
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