[gmx-users] g_sorient HELP!!!

[Ilya Chorny]

Thanks for the help.  I still get strange results for the configuration I
described. I see a contribution at 22.5 and 139.5. I would expect 0 or 180
and not both. What do you think is going on?

Thanks

Ilya

# This file was created by gmx-ana
# which is part of G R O M A C S:
# Getting the Right Output Means no Artefacts in Calculating Stuff
# All this happened at: Tue Oct 28 09:43:31 2003
#
@    title "Solvent orientation between 0 and 0.5 nm"
@    xaxis  label "Angle"
@    yaxis  label "Number"
@TYPE xy
@ subtitle "average shell size 1.0 molecules"
4.5 0 0.0784591
13.5 6.3662 0.233445
22.5 0 0.382683
31.5 0 0.522499
40.5 0 0.649448
49.5 0 0.760406
58.5 0 0.85264
67.5 0 0.92388
76.5 0 0.97237
85.5 0 0.996917
94.5 0 0.996917
103.5 0 0.97237
112.5 0 0.92388
121.5 0 0.85264
130.5 0 0.760406
139.5 6.3662 0.649448
148.5 0 0.522499
157.5 0 0.382683
166.5 0 0.233445
175.5 0 0.0784591



-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Berk Hess
Sent: Tuesday, October 28, 2003 2:33 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] g_sorient HELP!!!


>Hello All
>
>I great a gro file that looks like this
>
>test
>4
>     1ARR    ARR    1   1.750   2.500   2.500  0.0000  0.0000  0.0000
>     2SOL     OW    2   1.850   2.500   2.500  0.6290  0.3015 -0.0304
>     2SOL    HW1    3   1.900   2.550   2.500  0.8230 -0.5734  2.1610
>     2SOL    HW2    4   1.900   2.450   2.500  -0.2208  2.6625 -0.1271
>
>Then I run
>
>g_soreint -f test -s test.gro

I have found three bugs in g_sorient:

One is that even when -com has not been specified it calculates
the com of one particle, but with a gro or pdb file for -s the masses
have not been loaded. This explains the nan's in your output.
Using a tpr file for -s would circumvent this.

Another is that in the -o output the histogram has always been shifted
one bin to right. So even if you have masses you would get 0 in the
case of your gro file, as the angle is 180 and this shifts out on the right
side of the histogram. (All the other output files are correct)

Yet another bug is that -com just uses the coordinates of the first
particle in the group instead of the com of the group.

All these bugs have been fixed for the new release.

Berk.

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