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. Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham <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 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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