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.abra...@anu.edu.au
<mailto:mark.abra...@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.abra...@anu.edu.au <mailto:mark.abra...@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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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