[gmx-users] g_anaeig, entropy

[Yulian]

entropy_short_report.txt
<http://gromacs.5086.x6.nabble.com/file/n5013709/entropy_short_report.txt>  
entropy_long_report.txt
<http://gromacs.5086.x6.nabble.com/file/n5013709/entropy_long_report.txt>  

Dear David,

I attached two files with reports (detailed and short).
I checked two systems "ubc7" and "ACP".

1. For ubc7 I get the same entropy with 'pwd'/file and with ./file.
But it is different if I use different working stations.

2. For ACP the result is different if I use 'pwd'/file or ./file  and the
same if I use different working stations (but only fot ./file variant).

Please see the short report:

*ubc7:*
cassini: md100ns1> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
./eigenvec_ubc7_1-3_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is inf J/mol K
The Entropy due to the Schlitter formula is nan J/mol K


saturn: md100ns1> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
./eigenvec_ubc7_1-3_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 20626.8 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K


zeus: md100ns1> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
./eigenvec_ubc7_1-3_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 20151.9 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

####

*ACP:*

cassini: md20nsAll> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
./eigenvec_CUT6_10_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 10728 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

cassini: md20nsAll> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
/home_b/yulian/shlomi/CUT6/md20nsAll/eigenvec_CUT6_10_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is inf J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

#

saturn: md20nsAll> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
./eigenvec_CUT6_10_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 10728 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

saturn: md20nsAll> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
/home_b/yulian/shlomi/CUT6/md20nsAll/eigenvec_CUT6_10_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 10796.7 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

#

zeus: md20nsAll> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
./eigenvec_CUT6_10_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 10728 J/mol K

zeus: md20nsAll> /home_b/yulian/BIN/gromacs-4.5.6/bin/g_anaeig -v
/home_b/yulian/shlomi/CUT6/md20nsAll/eigenvec_CUT6_10_prot-H.trr -entropy
The Entropy due to the Quasi Harmonic approximation is 10559.3 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K









David van der Spoel wrote
> On 2014-01-08 17:25, Yulian wrote:
>> Dear Gromacs users,
>>
>> There is a problem with entropy calculations with g_anaeig.
>>
>> I try to calculate entropy using this:
>>
>> g_anaeig -v eigenvec.trr -entropy
> SO if you do
> 
> g_anaeig -v eigenvec.trr -entropy
> or
> g_anaeig -v `pwd`/eigenvec.trr -entropy
> you get a different result? that seems hard to believe unless there is a 
> random number generator at work, which there shouldn't be in this case.
> 
> If it is reproducible please post a redmine report.
> 
>>
>> But result (entropy value) is not the same if I just give the name of
>> file
>> or give the whole pass to the file.
>> The result is also different If I run this command from different work
>> stations.
>>
>> I use gromacs-4.5.6.
>>
>> I already asked this question before but it seems that nobody knew how to
>> deal with it. Or maybe I miss something in previous discussions?
>> Should I consider this effect as a gromacs bag?
>>
>> Thank you for any help
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://gromacs.5086.x6.nabble.com/g-anaeig-entropy-tp5013649.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.

> spoel at .uu

>     http://folding.bmc.uu.se
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View this message in context: http://gromacs.5086.x6.nabble.com/g-anaeig-entropy-tp5013649p5013709.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.