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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