Hi,The simulation box consists of layers of cyclohexane and vacuum. Ensemble is NVT.
The density profiles of cyclohexane for 5-10 ns, 10-15 ns and 15-20 ns coincide. However the density profile for 5-20 ns is significantly higher than the ones calculated.
g_density -n -b 5000 -e 20000If I calculate the 5-20 ns interval using every 5th frame the density profile resembles that of the 5-10, 10-15, 15-20 ns's.
g_density -n -b 5000 -e 20000 -dt 5 Attached is the graph of these profiles.I have tried this in 4.07, 4.5.3 and 4.5.4. The results are similar for all these versions.
I am aware that such inconsistencies may occur with g_density in NPT ensembles. However I am using a NVT ensemble. Is there something am I missing? And more importantly, how should I decide which one is the correct density?
Thanks, Cahit
<<attachment: dprof.png>>
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
