[gmx-users] trjorder not working
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.
> 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