[gmx-users] trjorder not working

shivangi nangia shivangi.nangia at gmail.com
Fri Apr 29 03:29:46 CEST 2011


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.

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.
> Mark
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