Hello, 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).
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): g_dipoles -f nvt10ns.xtc -s previous.tpr -corr mol -mu 1.75 *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* When I do this, I get the following output to terminal: There are 255 molecules in the selection Using volume from topology: 34.3361 nm^3 Last Frame 30000 time 12000.001 t0 0, t 12000, teller 30001 **then there is a long pause (approx 5 minutes)** Dipole Moment (Debye) ______________________ Average = 1.9194 Std. Dev. = 0.0085 Error = 0.0000 **Then it lists the different dipole moments, kirkwood factors, and finally an epsilon = 4.47756** (I won't bother to write all of the info down) I wanted to include the output files, but the e-mail was too big and wouldn't go through. I can send them later. It seems that the g_dipoles is working fine for me. 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: 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. eps0 - this is the epsilon of my liquid - but is it the epsilon that was calculated from g_dipoles (4.47756)? When I run the command: g_dielectric -f dipcorr.xvg -epsRF 0 -d -o -c I get a segmentation fault before anything happens: Read data set containing 2 columns a nd 15001 rows Assuming (from data) that timestep is 0.4, nxtail = 1249 Creating standard deviation numbers ... nbegin = 13, x[nbegin] = 5.2, tbegin = 5 Segmentation Fault 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. 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. c, line 466. I am probably missing something obvious, but I am having a hard time figuring out what it is. I appreciate any help. Thank you for your time, Jenny
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