g_dielectric segmentation fault
I calculated ACF of the total dipole moment of a box of SPC water molecules
(PME, 300K) by issuing:
g_dipoles -s prod_in.tpr -f prod_out.xtc -corr total
Then I used the resulting dipcorr.xvg file as an input to g_dielectric which I
run as follows:
g_dielectric -f dipcorr.xvg -epsRF 0 -ffn aexp
The meessage I got was the following:
Read data set containing 2 colums and 1501 rows
Assuming (from data) that timestep is 1, nxtail = 500
Creating standard deviation numbers ...
nbegin = 5, x[nbegin] = 5, tbegin = 5
Any feedback will be much appreciated
#4 Updated by David van der Spoel over 12 years ago
Sorry if you got this twice. I just reply to your previous bugzilla mail.
I compiled gmx on Fedora Core 6 x86_64 architecture with gcc-4.1.1-30.
Have you tried the rpms that are provided on the gmx website?
Or upgrading/downgrading the compiler? Or using e.g. the Intel compiler?
Alternatively if you compile with -g and run it in the debugger to see
where it crashes.
It would be very usefull if you could help figure out the steps that
makes to calculate the frequency dependent dielectric constant. I will try to
repeat them "manually" (e.g. in Mathematica).
So it first fits the ACF to, say, an exp, then performs the numerical
then Laplace-Fourier transform? Is this the right order? Can we do the
the transform without prior fitting. This is if we simulate a polymer or a
than a simple polar Debye liquid like water.
It is described in JCP paper.
The largest problem is the smooth transition from ACF to fitted curve.
This was definitely done prior to taking the derivative.