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
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
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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