[gmx-users] Re:gmx-users Digest, Vol 42, Issue 36
luciano.pgomes at uol.com.br
Wed Oct 10 17:36:09 CEST 2007
I used -DPOSRE, no constraints but temperature coupling (berendsen), no pressure coupling.
> 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
> > Thanks,
> > Luciano
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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