[gmx-users] Use of g_dielectric
G.N.Patargias at leeds.ac.uk
Wed Mar 14 21:12:17 CET 2007
Thanks for your reply David. I am trying to understand how
fitting but it is not very clear from the paper and g_dielectric -h.
For example, why do I get a segmentation fault when I issue:
g_dielectric -f dipcorr.xvg -epsRF 0 -ffn aexp -bfit 0 -eint 10
Read data set containing 2 colums and 1261 rows
Assuming (from data) that timestep is 1, nxtail = 500
Creating standard deviation numbers ...
nbegin = 0, x[nbegin] = 0, tbegin = 0
Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Wed 3/14/2007 6:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Use of g_dielectric
Georgios Patargias wrote:
> What does g_dielectric take as an input? Is it the total dipole moment of a system
> or is the ACF of the total dipole moment?
> The manual suggests the Mtot.xvg for input but it explicitly mentions the ACF which
> is consistent with the J.Phys.Chem paper. Which one should be used?
the autocorrelation of the total dipole.
> I am not sure I can understand the meaning of the -efit, -eint and -tail flags.
> What values should these flags have in order to get reasonble (compared to
> theJ.Phys.Chem paper) diel. properties for a PME SPC water simulation.
as decribed in the JCP paper one can do the fitting in several ways, and
part of it involved assuming en exponential long time correlation, and
slowly converting from the data to the fit.
g_dielectric -h says:
-eint real 5 Time were to end the integration of the
start to use the fit
-bfit real 5 Begin time of fit
-efit real 500 End time of fit
-tail real 500 Length of function including data and tail from
> Thanks a lot in advance.
> Dr. George Patargias
> Polymer IRC Group
> University of Leeds
> Leeds, LS2 9JT, UK
> gmx-users mailing list gmx-users at gromacs.org
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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