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 <jalem...@vt.edu
<mailto:jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto: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>
<mailto: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 <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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