[gmx-users] g_order question

[David van der Spoel]

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