HI David, I used -DPOSRE, no constraints but temperature coupling (berendsen), no pressure coupling.
thanks, Luciano > luciano.pgomes wrote: > > Hi, > > > >> Hi All, > >> > >> I had this problem running MD on a single Debian machine: > >> > >> Program mdrun_d, VERSION 3.3.1 > >> Source code file: stat.c, line: 257 > >> > >> Fatal error: > >> XTC error > >> > >> > >> There is no chance of being size exceeded of file or quota, or disk error. > >> I compiled gromacs with gcc-3.4... > >> > >> Does anyone know what this error means? Gcc version may be the cause? > >> > >> Thanks, > >> > >> Luciano P Gomes > >> > >> > > > >> it can also mean that your system is exploding. > >> > > No. > > The xtc file doesn't opened. It crashed VMD. > > > > I forgot saying that I was running simulated annealing protocol with a DNA > > molecule and crystallographic water molecules (HOH) freezed, only moving > > ions and water molecules placed by genbox (tip3p). The crash occured on 2 > > ps of simulation time in a temperature of 50K. I had excluded non-bonded > > interactions: DNA DNA HOH DNA HOH HOH. > > > > I am running now a simple MD at 300K and this error haven't occured yet. > > I am trying to understand... > > did you use pressure coupling? you can not have Pcoupl with freezing and > constraints. > > > > > > Thanks, > > Luciano > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
