[gmx-users] question about dielectric constant calculation
David van der Spoel
spoel at xray.bmc.uu.se
Fri Mar 31 09:15:41 CEST 2006
Lei Zhou wrote:
> Dear GMX-users,
> I am trying to calculate the dieletric constant based on MD
> trajectories. Two programs are used, g_dipoles and g_dielectric. I have
> the following questions:
> 1) In g_dipoles, what number should I use for the flag -epsilonRF? I
> used PME duing MD simulation with the epsilon-r as 1 and epsilon-surface
> as 0.
In that case 0
> 2) What other flags are critical for calculation, like -P, Order of
> Legendre polynomial for ACF?
If you want to compute ACF, then P 2 could be used. Please refer to my
paper, J Chem Phys 108 (1998) 10220-10230
> 3) Based on the manual, the epsilon calculated by g_dielectric is
> frenquency-related. How about the epsilon output from g_dipoles and the
> relationship to difference frenquencies?
To get frequency dependent epsilon, you need to run g_dielectric (see
> 4) I used the output from g_dipoles, Mtot.xvg, as an input for
> g_dielectric. Here is the command used: g_dielectric -f Mtot.xvg,
> however, I got the following error messages after frame 49: Fatal error:
> nparm = 0 in file expfit.c, line 462.
Is Mtot.xvg OK?
You shouldn't get fatal error unless Mtot.xvg contains weird data. If
you have checked Mtot.xvg and it is fine please submit a bugzilla.
> I am really grateful for any help with those questions. Thank you.
> Lei Zhou
> Columbia University
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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