AMBER Archive (2009)

Subject: [AMBER] ptraj quasiharmonic analysis

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Tue Jun 09 2009 - 01:38:01 CDT


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?

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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