[gmx-users] Re:gmx-users Digest, Vol 42, Issue 36
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 listgmx-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 listgmx-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
[gmx-users] xtc error
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... Thanks, Luciano ___ gmx-users mailing listgmx-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
[gmx-users] xtc error
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 ___ gmx-users mailing listgmx-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
[gmx-users] reporting failure
Reporting... Program mdrun_d, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 560 ] Please report this to the mailing list (gmx-users@gromacs.org) Luciano Gomes ___ gmx-users mailing listgmx-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
