[gmx-users] Schlitter Configurational entropy 'NaN'

David van der Spoel spoel at xray.bmc.uu.se
Thu May 15 10:00:29 CEST 2014

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 

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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