[gmx-users] trjorder not working
Justin A. Lemkul
jalemkul at vt.edu
Fri May 6 16:42:14 CEST 2011
shivangi nangia wrote:
> 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?
>
If they all have different numbers of atoms, no.
> or I have have to play around ordering them one by one?
>
Probably. If your goal is to set up a spherical system, there are probably far
easier ways to do this with genbox -shell and/or VMD/NAMD solvation procedures
to build spheres.
-Justin
> Thanks,
> SN
>
>
> On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>
> <mailto: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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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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