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 [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 ----------------------------------------------- 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 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
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