[gmx-users] xtc error
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 10 16:56:56 CEST 2007
>> 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?
>> Luciano P Gomes
>> it can also mean that your system is exploding.
> 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
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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