[gmx-users] Schlitters entropy calculation

David van der Spoel spoel at xray.bmc.uu.se
Fri May 27 18:15:07 CEST 2011

On 2011-05-27 18.11, Bala subramanian wrote:
> Friends,
> I am a newbie to gromacs, trying to calculate the Schlitters entropy
> calculation using the following commands.
> g_covar -f  mytraj.xtc  -s  structure.pdb -n index.ndx -b 0 -e 4000 -mwa
> -ref
> g_anaeig -entropy  -temp 300
The formula contains many logarithms. Maybe one of them get zero as an 
argument. Please check the source code to debug this.

> When i used the above commands, i get the Schlitter entropy value for
> the 4000 frames, but if i use less than 4000 frames, the program does
> not calculate the entropy value and it shows the following result. This
> happens irrespective of the region i select from the trajectory or the
> subset of atoms i choose for the calculation. I am using gromacs version
> 4.5.3. I have the same problem even with previous version of gromacs.
> The Entropy due to the Quasi Harmonic approximation is 14895 J/mol K
> The Entropy due to the Schlitter formula is nan J/mol K
> Any suggestion on what could be going wront.
> Bala

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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