[gmx-users] Schlitter Configurational entropy 'NaN'
David van der Spoel
spoel at xray.bmc.uu.se
Thu May 15 10:36:18 CEST 2014
On 2014-05-15 10:30, tarak karmakar wrote:
> Dear Sir,
> Thanks for the quick reply.
> Using g_anaeig_d I've got both of them as 'nan'
> The Entropy due to the Quasi Harmonic approximation is -nan J/mol K
> The Entropy due to the Schlitter formula is nan J/mol K
Interesting. Is your system far out of equilibrium? Do the eigenvalues
look reasonable? Or is your system very large?
> On Thu, May 15, 2014 at 1:30 PM, David van der Spoel
> <spoel at xray.bmc.uu.se>wrote:
>> On 2014-05-15 09:07, tarak karmakar wrote:
>>> Dear All,
>>> I wanted to calculate configurational entropy of a protein by using
>>> and g_anaeig as follows,
>>> g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr -av
>>> g_anaeig -v eigenvec.trr -entropy -temp 300
>>> I got the following results
>>> The Entropy due to the Quasi Harmonic approximation is 31440.3 J/mol K
>>> The Entropy due to the Schlitter formula is nan J/mol K
>>> I went back to check the eigenvector file by dumping it to a new file
>>> 'dump'. There is no 'nan' indeed.
>>> Could anyone comment on why I'm getting Schlitter entropy as 'nan'?
>>> Thanks and regards,
>>> Numerical error due to large numbers. Try compiling gromacs in double
>> 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 xray.bmc.uu.se http://folding.bmc.uu.se
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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 xray.bmc.uu.se http://folding.bmc.uu.se
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