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) 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) ?? If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend. 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>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>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 >> > > > > -- > 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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