AMBER Archive (2009)

Subject: Re: [AMBER] ptraj quasiharmonic analysis

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Tue Jun 09 2009 - 02:19:23 CDT

I think you are looking into the wrong file. What you pasted below is
obviously from the file called 'mwcovar1' (contains the average
coordinates of your chosen subset of atoms and the frequencies for each
mode). But the thermochemistry is written to standard output which
means that you better capture ptraj's output in a file.

On Tue, 2009-06-09 at 14:38 +0800, Neha Gandhi wrote:
> Dear List,
>
> I have the following script
>
> trajin xx.mdcrd 1 50 1
> strip :WAT
> strip :Na+
> image
> rms first *
> matrix mwcovar name mwcovar1 out mwcovar1
> analyse matrix mwcovar1 thermo out thermo
>
> How do I interpret the output in terms of -TdeltaS in kcal/mol? Can you
> explain me the output. The output file looks something like this..
>
> Eigenvector file: MWCOVAR
> 7245 7245
> 47.60873 39.89070 33.06393 47.84174 39.95691 33.04234
> 47.81734
> .............................
> ****
> 1 1.13384
> ****
> 2 1.69121
> ****
> 3 1.96724
> ****
> 4 2.10823
> ****
> ......................
>
> Did I miss something out? What values represent the entropy in kcal/mol?
>
>

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