Hello, have you tried g_current ? It also calculates the dielectric constant.
/Flo On 27.07.10 02:36, Jennifer Casey wrote: > 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 cannot attach the output files since they too make this e-mail too > big. I will send them if requested.) > > 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 and 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 -- Florian Dommert Dipl. Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70565 Stuttgart Germany Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !!
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