t.piggot at soton.ac.uk
Tue Jun 5 16:52:57 CEST 2012
I think Erik meant to say that the program is trjorder (not g_order) for
the ordering of molecules by distance.
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.
> 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.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
>> 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-request at 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
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
Dr Thomas Piggot
University of Southampton, UK.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users