[gmx-users] trjorder not working
shivangi nangia
shivangi.nangia at gmail.com
Fri May 6 16:39:43 CEST 2011
Thanks Justin, that was helpful.
I have a following question.
Since in my system I have both methanol and water and I want to order both
of them ( my eventual aim to make a sphere), is there is way to override -na
option ( for water na 4, methanol 3).
Is there is way that all the components of the system get ordered with
respect to the protein?
or I have have to play around ordering them one by one?
Thanks,
SN
On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> shivangi nangia wrote:
>
>> 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)
>>
>>
>>
> I suspect your index file is wrong. Presumably, you have measured
> distances to individual water molecules using g_dist, which would require a
> custom index group for each water molecule analyzed, correct? If you use
> ordered.gro, the residue numbers will indeed be scrambled based on ordering,
> but the distance will correspond to the original distance, not the ordered
> one.
>
> The solution is to use your unordered coordinate file or .tpr file to
> create the index group, then perform the distance measurements.
> Alternatively, use genconf to renumber ordered.gro to get sequential
> residue numbers, then create whatever index file you might need from the
> renumbered coordinate file.
>
>
>
>>
>>
>> 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) ??
>>
>>
> As the documentation is written, yes.
>
>
> If so, then tha talso generates a .gro file which produces random water
>> molecules but there is again no trend.
>>
>>
> Same problem as above, I suspect.
>
> -Justin
>
> 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<mailto:
>> 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 <mailto: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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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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