[gmx-users] g_order question

[David van der Spoel]

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