[gmx-users] g_order question

[Paymon Pirzadeh]

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


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