Hello,<br>
<br>
I am trying to calculate the dielectric constant for pure
tetrahydrofuran (THF) at 298K. I keep running into problems though. I
have looked through the gmx user list to see if others have had these
problems, but I didn't see any mention of them (although I did see that
others were asked to report issues with g_dipoles to bugzilla).<br>
<br>
The first thing I do is run g_dipoles using the command (I do this in order to get the ACF to use in g_dielectric):<br>
g_dipoles -f nvt10ns.xtc -s previous.tpr -corr mol -mu 1.75 <br>
*I would have liked to attach the tpr and xtc file, but the message was too big. I can send them if they will help*<br>
When I do this, I get the following output to terminal:<br>
<pre style="margin: 0em;"><br></pre>
There are 255 molecules in the selection<br>
Using volume from topology: 34.3361 nm^3<br>
Last Frame 30000 time 12000.001<br>
t0 0, t 12000, teller 30001<br>
**then there is a long pause (approx 5 minutes)**<br>
Dipole Moment (Debye)<br>
______________________<br>
Average = 1.9194 Std. Dev. = 0.0085 Error = 0.0000<br>
<br>
**Then it lists the different dipole moments, kirkwood factors, and finally an epsilon = 4.47756**<br>
(I won't bother to write all of the info down)<br><br>I wanted to include the output files, but the e-mail was too big and wouldn't go through. I can send them later.<br>
<br>
It seems that the g_dipoles is working fine for me.<br>
<br>
<br>
Once I have the autocorrelation function (dipcorr.xvg), I want to use
g_dielectric. Before I talk about the problems I have here, I wanted
to verify a few things about the various options:<br>
epsRF - the default here is 78.5, even though the default in g_dipoles
is 0 (infinity). I wanted it to be infinity, so I assume I change it.<br>
eps0 - this is the epsilon of my liquid - but is it the epsilon that was calculated from g_dipoles (4.47756)?<br>
<br>
When I run the command:<br>
g_dielectric -f dipcorr.xvg -epsRF 0 -d -o -c<br>
I get a segmentation fault before anything happens:<br>
Read data set containing 2 columns a nd 15001 rows<br>
Assuming (from data) that timestep is 0.4, nxtail = 1249<br>
Creating standard deviation numbers ...<br>
nbegin = 13, x[nbegin] = 5.2, tbegin = 5<br>
Segmentation Fault<br>
<br>
If I leave out the -epsRF, I still get the same error. If I include
eps0, I still get a segmentation fault. It seems strange to me since
GROMACS generates the input and yet has an issue with it.<br><br>I
would like to point out that the manual states to use dipcorr.xvg to
get the dielectric constant, but after reading the paper GROMACS
references, it seems that <Mtot^2> is more appropriate. I tried
running the command g_dielectric -f Mtot.xvg, and the segmentation
fault went away. Instead lambda went to infinity and there was a fatal
error (nparm = 0 in the file ../../../../src/tools/exptfit.<div id=":169" class="ii gt">c, line 466.<br>
<br>
I am probably missing something obvious, but I am having a hard time figuring out what it is. I appreciate any help.<br>
<br>
Thank you for your time,<br>
Jenny
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