[gmx-users] Use of g_dielectric

[Georgios Patargias]

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
Segmentation fault

George

Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK



-----Original Message-----
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:
> Hi 
> 
> 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 
data and
                             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
                             fit

> 
> Thanks a lot in advance.
> George
> 
> Dr. George Patargias
> Polymer IRC Group
> University of Leeds
> Leeds, LS2 9JT, UK
> 
> 
> 
> -
> 
> 
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-- 
David.
________________________________________________________________________
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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