[gmx-users] g_order question

[Paymon Pirzadeh]

I tried the -Sg and it worked. Thanks.
But, I used -Sgsl for a spatial profile and it looks like that it is not
a valid option. I tried the following:
 
g_order_d_mpi -f Ih0001_54_62_102.xtc -n wateroxygens.ndx -s
Ih0001_54_62_102.tpr -os Ih0001_54_62_102-sg -sl 100 -d z

but I ran into the previous segmentation fault. 
If I just use the Sg, just the temporal profile is generated which is
not what I want.
Sorry for mass of e-mails, but any tips on that?

Paymon

On Tue, 2010-08-31 at 21:49 +0200, David van der Spoel wrote:
> On 2010-08-31 21.19, Paymon Pirzadeh wrote:
> > 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
> You need to replace -o by one of
>   -Sg     sg-ang.xvg  Output, Opt. xvgr/xmgr file
>   -Sk    sk-dist.xvg  Output, Opt. xvgr/xmgr file
> -Sgsl sg-ang-slice.xvg  Output, Opt. xvgr/xmgr file
> -Sksl sk-dist-slice.xvg  Output, Opt. xvgr/xmgr file
> 
> >
> >
> >
> > 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
> >
> 
> 
> -- 
> 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