[gmx-users] Re:gmx-users Digest, Vol 42, Issue 36

[luciano.pgomes]

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
> > 
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> 
> 
> -- 
> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>