On 2010-10-16 21.36, Chih-Ying Lin wrote:
Hi
I issue the g_dipole command on Gromacs => And, the following
information is shown.
There are 10 molecules in the selection,
Does the Average =32.1611 refer to the average for a single over the
simulation time?
Or, the Average = 32.1611 summing for all the 10 molecules over the
simulation time?
If the average = 32.1611 for a single molecule with 33 atoms / united
atoms of most carbon groups, isn't the dipole moment too high?
I think this is the average per molecule. You may need to run trjconv
-pbc whole, because mdrun may break molecules in two parts, meaning that
the molecule becomes as big as the box.
What does "will subtract their charge at their center of mass" this mean?
Why "will subtract their charge at their center of mass" ?
==================================================================
There are 10 molecules in the selection
There are 10 charged molecules in the selection,
will subtract their charge at their center of mass
Using Volume from topology: 220.317 nm^3
Back Off! I just backed up epsilon.xvg to ./#epsilon.xvg.1#
Back Off! I just backed up aver.xvg to ./#aver.xvg.1#
Last frame 10000 time 20000.000
Average volume over run is 221.043
Dipole moment (Debye)
---------------------
Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095
--
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
--
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
