[gmx-users] Trajectories

Erik Marklund erikm at xray.bmc.uu.se
Tue Jun 5 15:41:43 CEST 2012

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.


> -- 
> ========================================
> 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
> ========================================
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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

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