[gmx-users] Trajectories

[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

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 <mailto: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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