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
same paper)
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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