[gmx-developers] Total dipole incorrect in energy file

[David van der Spoel]

Hi,

it used to be so that mdrun did not break molecules. However, nowadays 
it does, even though they are fixed before writing the coordinates. I 
suspect however that the broken molecules are not fixed before computing 
the total dipole, which is stored in the energy file. The total dipole 
is used for computing the dielectric constant in g_dipoles.

With the current g_dipoles I get good dielectric constants when using 
the coordinates, and insane (500) when using the energy file.

If this observation is correct we can do two things:
- fix the coordinates at every step before computing the total dipole
- not compute abd save the total dipole at all and remove the -en option 
from g_dipoles

I guess the decision depends on whether the CPU time for reconstrucing 
the molecules before computing the total dipole is large or not. Maybe 
Berk can comment on that, obviously there is a reason for not doing it 
every step.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se