On 2011-03-31 09.25, Dommert Florian wrote:
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number of sims.
How much long I should run the simulation.
until the average converges.
Nilesh
On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote:
On 2011-03-30 18.54, Nilesh Dhumal wrote:
Hello,
I am trying to calculate the dipole moment autocorrelation
function for my system (ionic liquid). I am using gromacs 4.0.7 version.
Hello,
I think you will get into some trouble when you try to calculate an
autocorrelation function of property that is not continuous in time. In
an ionic liquid you have contributions of the molecular dipole and
contribution of the charged molecules to the dipole. The latter part is
unfortunately not continuous due to jumping of the molecules over the
PBCs. It depends what kind of property you want to calculate, but we
experienced that simulations in the range of 50-100ns are required to
reliably determine properties like the dielectric constant. The next
point is that you have to save your coordinates and velocities quite
often ( every 0.02ps we used)
Check corresponding literature for further advice.
Thanks Florian, for pointing that out. I forgot about it in my previous
mail. In order to compute the dielectric constant one could in principle
apply constant electric fields at different strengths and then
extrapolate to zero. Don't know whether that has been done.
Cheers,
Flo
I run the simulation for 4 ns. I run the following command to
calculate the dipole moment autocorrelation function
g_dipoles -f water.trr -s water.tpr -corr total -c
The function is not geting converge to zero.
I want to use this data for calculation of power spectra by fourier
transfom of dipole moment autocorrelation function.
Can you tell why its not geting converge to zero?
You have to simulate at least a few 10s of ns for such slow liquids to
converge. Alternatively you can average over many independent simulations
(10s).
Thanks
Nilesh
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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--
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
--
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
--
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