[gmx-users] Schlitter Configurational entropy 'NaN'

[tarak karmakar]

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

Tarak


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
>> g_covar
>> and g_anaeig as follows,
>>
>> g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr -av
>> average.pdb
>> 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,
>> Tarak
>>
>>  Numerical error due to large numbers. Try compiling gromacs in double
> precision.
>
> --
> 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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