[gmx-users] g_dipoles
Viswanadham Sridhara
muta.mestri at gmail.com
Thu Nov 17 21:26:54 CET 2005
Thanks again David.
tpbconv was very useful instead of re-running the simulations and I could
find the dipole moment of the two groups separately and very quickly
..........
I have one more quick question related to this course of emails about
g_dipoles.
Once dipole moment of some biomolecule is calculated, what is a better way
of finding the permittivity of such cluster of homogeneous molecules.
In a better sense, did anyone tried to find the permittivity of the lipid
tails using gromacs??. I know g_dielectric command can help one to find
permittivity, but I find more appropriate and easier if I calculate
dielectric constant from dipole moment using Clausius-Mossotti relation.
I just wanted to know how to find permittivity of such complex, and are
there any other equations which helps me to find the permittivity of
lipids(without headgroups)??
Best regards,
Viswam.
On 11/15/05, David <spoel at xray.bmc.uu.se> wrote:
>
> On Tue, 2005-11-15 at 14:33 -0500, Viswanadham Sridhara wrote:
> > Thanks David.
> > One more quick question.
> > g_dipoles takes the molecule number unlike atom number for g_density.
> > So if I ran a simulation, is there any way out later to divide the
> > molecule into 2 seperate entities and find the dipole moment for these
> > 2 entities.
> > In other words if i ran the simulation with one kind of molecule which
> > has a head and tail, and later I want to seperately calculate the
> > dipole moment for the head and for the tail, is there any other way
> > instead of re-running the entire simulation by dividing these two
> > groups.......
> > (((( A has B and C entities, I want to find the dipole moment of B
> > and C separately. ))))
> > I hope my question is clear...
>
> As with perl, there are many ways to do things. Finding out how many is
> left as an exercise for the reader.
>
> To start of with, you can use tpbconv to create a tpr file in which all
> but the charges your are interested in are zero. Note that you want
> neutral groups, otherwise the meaning of the dipole is undefined.
>
> A second, somewhat more difficult possibility is to make a new topology
> with different molecule definitions.
>
>
> > Thanks,
> > Viswam.
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