[gmx-users] trjorder not working
shivangi.nangia at gmail.com
Thu May 5 22:27:01 CEST 2011
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
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
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
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:
> 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
> 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
> Am I wrong?
> 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.
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users