On 8/06/2011 9:41 PM, cdalgicdir wrote:
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 20000
If 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?
I'd guess this is an artefact of the fact that the times in the
trajectory file are not exactly multiples of the time step. That is just
life - see
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. If so,
one or more of these ranges is probably not computing over the set of
frames you think it is. Consider using suitable non-integers for -b and
-e, and avoiding -dt unless you know it will work on the times that
exist. trjcat -settime can help, also.
Mark
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
