[gmx-users] g_dielectric problem
Guilherme Duarte Ramos Matos
gduarter at uci.edu
Tue May 6 21:57:45 CEST 2014
Dear GROMACS users community,
I'm working with water solutions of small organic molecules and I am
interested in their dielectric spectra. After submitting the trajectory
file to g_dipoles and getting the dipcorr.xvg file, I'm facing some issues
when using g_dielectric. I've been using:
g_dielectric -f dipcorr.xvg -ffn exp_exp
the program runs but I get this worrisome message:
"Read data set containing 2 colums and 12501 rows
Assuming (from data) that timestep is 0.1, nxtail = 5000
Creating standard deviation numbers ...
nbegin = 50, x[nbegin] = 5, tbegin = 5
Step chi^2 Lambda A1 A2 A3 A4
irow = 2, icol = 2
nan nan nan
nan 0.000 nan
nan nan nan
Numerical Recipes run-time error...
GAUSSJ: Singular Matrix-2
Fit failed!
DATA INTEGRAL: 3.5, tauD(old) = 5.2 ps, tau_slope = 0.0, tau_slope,D
= 0.0 ps
tau_D from tau1 = 1.77e-26 , eps(Infty) = 80.000
nbegin = 50, x[nbegin] = 5, tbegin = 5
Making smooth transition from 50 through 53
SMOOTH integral = 3.61438e+00
FIT INTEGRAL (tau_M): 3.6, tau_D = 5.4
Doing FFT of 32768 points
MAXEPS = 5.18410e+01 at frequency 3.60107e+01 GHz (tauD = 4.4 ps)"
Can someone help me understand what should I do if I want g_dielectric to
do this fit for me? The other problem I'm facing is that the dielectric
spectrum looks like a NMR FID instead of the usual shape. What did I miss
there?
I tried to attach dipcorr.xvg, derive.xvg and epsw.xvg but unfortunately
the email was too big.
Sorry for the inconvenience
~ Guilherme
*****************************************************
Guilherme D. R. Matos
Graduate Student at UC Irvine
*****************************************************
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