[gmx-users] Trajectories

[Erik Marklund]

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
>>> 
>>> ========================================
>>> -- 
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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
>> http://www2.icm.uu.se/molbio/elflab/index.html
>> 
>> 
>> 
> 
> -- 
> Dr Thomas Piggot
> University of Southampton, UK.
> -- 
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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
http://www2.icm.uu.se/molbio/elflab/index.html

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