5 jun 2012 kl. 16.52 skrev Thomas Piggot: > Hi, > > I think Erik meant to say that the program is trjorder (not g_order) for the > ordering of molecules by distance. > > Cheers > > Tom
Indeed I did. Sorry, and thanks for the correction. Erik > > On 05/06/12 14:41, Erik Marklund wrote: >> >> >> 5 jun 2012 kl. 15.05 skrev Justin A. Lemkul: >> >>> >>> >>> On 6/5/12 9:02 AM, rankinb wrote: >>>> I am interested in pulling out the trajectories (x,y,z coordinates) of >>>> water >>>> molecules within a certain distance of my solute molecule. I have tried >>>> using g_select, but that will only give me the atom numbers and not the >>>> trajectories. I can create an index file using this command but >>>> unfortunately each time frame is set as a different group. >>>> >>>> Is there a way to get the trajectories at all frames of only the water >>>> molecules within a specified distance of a solute molecule? >>>> >>> >>> At present, there is no elegant way to construct such a trajectory, since, >>> in principle, each frame can have a different number of atoms >>> based on which water molecules satisfy the given criteria. Each index >>> group that g_select provides corresponds to an individual frame in the >>> original trajectory, which you can use to pull out individual coordinate >>> files. Perhaps a multi-frame .pdb or .gro file would work, but I believe >>> that .xtc and .trr files have to have the same number of atoms in each >>> frame to be interpreted correctly. >>> >>> -Justin >> >> g_order orders the molecules according to distance to solute. Then you can >> pick out the N first from each frame. It is, however, a bit cumbersome for >> an entire trajectory. >> >> Erik >> >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> 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 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 >> >> ----------------------------------------------- >> Erik Marklund, PhD >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: +46 18 471 6688 fax: +46 18 511 755 >> er...@xray.bmc.uu.se >> http://www2.icm.uu.se/molbio/elflab/index.html >> >> >> > > -- > Dr Thomas Piggot > University of Southampton, UK. > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
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