[gmx-users] g_order question

[Paymon Pirzadeh]

Here is the command:

g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s
265K_50_50_50_2.tpr -o Sg265K



On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote:
> On 2010-08-31 21.10, Paymon Pirzadeh wrote:
> > Yes,
> > I tried it, but I run into segmentation fault. Here is part of the error
> > message:
> >
> > WARNING: distance between atoms 4869 and 0>  0.3 nm (3.515866). Index
> > file might be corrupt.
> > WARNING: distance between atoms 4870 and 0>  0.3 nm (3.580329). Index
> > file might be corrupt.
> > WARNING: distance between atoms 4871 and 0>  0.3 nm (3.489775). Index
> > file might be corrupt.
> > WARNING: distance between atoms 4872 and 0>  0.3 nm (3.464816). Index
> > file might be corrupt.
> > WARNING: distance between atoms 4873 and 0>  0.3 nm (3.561426). Index
> > file might be corrupt.
> > Segmentation fault
> >
> what command line are you using?
> 
> >
> > I thought it might be a periodic boundary issue, so I issued:
> >   trjconv_d_mpi -f 265K_50_50_50_2.xtc -o 265K_50_50_50_2-pbcfixed -pbc
> > whole -s 265K_50_50_50_2.tpr
> >
> > but the problem still persists. Any tips?
> > Regards,
> >
> > Paymon
> >
> >
> >
> >
> >
> > On Tue, 2010-08-31 at 20:37 +0200, David van der Spoel wrote:
> >> On 2010-08-31 20.26, Paymon Pirzadeh wrote:
> >>> Hello,
> >>> It is said in the mannual that g_order compute the order parameter per
> >>> atom for carbon tails. Can it also calculate order (degree of
> >>> tetrahedrality) for water molecules if only water oxygens are selected
> >>> in index file? The reference paper is for water molecules though. Also,
> >>> does it calculate an average value or give a profile as a function of
> >>> time?
> >>> thanks,
> >>>
> >>> Paymon
> >>>
> >> Have you tried it?
> >>
> >> You can compute tetrahedrality for water, and also do it in slices
> >> accross the box axis. It computes the average over time.
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Dept. of Cell&  Molec. Biol., Uppsala University.
> >> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> >> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se