On Mon, Dec 03, 2012, marawan hussain wrote:
>
>
> I think if this was the case i will see the box simply shrink but no
> change either in density or dipole moment..
If the box shrinks then the density has to increase, since you have a fixed
number of molecules.
> the box enlarges and dipole moment changes..my feeling is that the cubic
> cell is somehow disfigured..indeed the longer the simulation the less
> cubic the box...if you have other suggestions please tell...thanks for
> the paper...
You don't say how much the dipole moment changes, but running for just 1ps
is not long enough to equilibrate the system. Distorion of the cell is just
an imaging artifact: see the "image" command in ptraj or cpptraj. Try using
the dftb Hamiltonian to run for much longer times, in order to get an idea of
what to expect for equilibration.
...good luck...dac
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Received on Mon Dec 03 2012 - 05:00:03 PST
