[gmx-users] trjorder not working

[shivangi nangia]

Hello,

Came back to the set of calculations I was doing few days back.

I have a box of water (TIP4P), methanol, protein and DHB anions.

I minimized this system.

Trying to use trjorder for water molecules with respect to the protein
(eventually I want to make a sphere by ordering and getting rid of the
molecules I do not want)

In the index.ndx file i specified atom "144" (belongs to protein)

so when I run

 trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro

I pick number associated with atom "144" and SOL ( tip4p water) and I
generate ordered.gro

The sequence for SOL changes ( random), but when I use g_dist as I go down
the ordered.gro, there is still no trend ( ascending with respect to
protein)





Also, -da 0 refers to an atom OR COM of the molecule.
using   trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro
and running it

and choosing "1" for protein and "14" for SOL means that gromacs
automatically understands that protein's COM is to be used to order SOL
(tip4p, -na 4) ??

If so, then tha talso generates a .gro file which produces random water
molecules but there is again no trend.

I am very confused about using trjorder, it will be really helpful if
someone or Mark can help me understand.

Thanks a lot
SN


On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 4/29/2011 11:29 AM, shivangi nangia wrote:
>
> Hello,
>
> The manual explaining trjorder says:
>
> trjorder orders molecules according to the smallest distance to atoms in a
> reference group or on z-coordinate (with option -z). With distance
> ordering, it will ask for a group of reference atoms and a group of
> molecules. For each frame of the trajectory the selected molecules will be
> reordered according to the shortest distance between atom number -da in
> the molecule and all the atoms in the reference group. *The center of mass
> of the molecules can be used instead of a reference atom by setting -da to
> 0*
>
> In order to arrange water molecules in accordance with the COM of the
> polypeptide, I chose -da 0.
>
>
> As it says above, -da refers to an atom or COM of the molecule, not the
> reference group. This could be worded better in the documentation.
>
> Be sure you're choosing the groups you think you are choosing - you not
> copying relevant parts of your terminal output into emails is making things
> difficult.
>
> Mark
>
>
> Am I wrong?
>
> Thanks,
> SN
>
>
>
>
> On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>> On 4/29/2011 4:08 AM, shivangi nangia wrote:
>>
>>> Hello all,
>>>
>>> I am trying to order the TIP4P water molecules in my system with respect
>>> to the polypeptide in my system.
>>>
>>> The command I am using is:
>>>
>>>  trjorder -f shape.gro -s shape.tpr -da 0  -na 4 -o ordered.gro
>>>
>>> This runs without any error and ordered.gro is generated with random
>>> sequence of water molecules.
>>>
>>> Just to cross check I calculated the distances between one of atoms of
>>> the polypeptide and oxyegn atom of different "ordered" water molecules.
>>> I found, there is no ascendig trend in the distances with respect to the
>>> polypeptide as a go down in the "ordered.gro" file.
>>>
>>> What could be going wrong?
>>>
>>
>> -da 0 has a particular effect - is it appropriate? Did you choose the
>> right groups? You could use the -nshell option to probe what trjorder thinks
>> is going on.
>>
>> Mark
>>
>>
>>
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>
>
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