Thanks Justin, that was helpful. I have a following question.
Since in my system I have both methanol and water and I want to order both of them ( my eventual aim to make a sphere), is there is way to override -na option ( for water na 4, methanol 3). Is there is way that all the components of the system get ordered with respect to the protein? or I have have to play around ordering them one by one? Thanks, SN On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul <[email protected]> wrote: > > > shivangi nangia wrote: > >> 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) >> >> >> > I suspect your index file is wrong. Presumably, you have measured > distances to individual water molecules using g_dist, which would require a > custom index group for each water molecule analyzed, correct? If you use > ordered.gro, the residue numbers will indeed be scrambled based on ordering, > but the distance will correspond to the original distance, not the ordered > one. > > The solution is to use your unordered coordinate file or .tpr file to > create the index group, then perform the distance measurements. > Alternatively, use genconf to renumber ordered.gro to get sequential > residue numbers, then create whatever index file you might need from the > renumbered coordinate file. > > > >> >> >> 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) ?? >> >> > As the documentation is written, yes. > > > If so, then tha talso generates a .gro file which produces random water >> molecules but there is again no trend. >> >> > Same problem as above, I suspect. > > -Justin > > 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 >> <[email protected]<mailto: >> [email protected]>> 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 >>> <[email protected] <mailto:[email protected]>> 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 [email protected] >>> <mailto:[email protected]> >>> >>> 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 [email protected] >>> <mailto:[email protected]>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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