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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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