[gmx-users] g_anaeig, entropy
Yulian
zzeppelin87 at gmail.com
Sun Jan 12 11:35:11 CET 2014
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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to
> gmx-users-request@
> .
--
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.
More information about the gromacs.org_gmx-users
mailing list